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package prok;
import java.util.Arrays;
import shared.Tools;
import stream.Read;
import structures.ByteBuilder;
import structures.LongHashSet;
class StatsContainer {
/*--------------------------------------------------------------*/
/*---------------- Initialization ----------------*/
/*--------------------------------------------------------------*/
StatsContainer(int type_, int kInner, int framesInner, int kStart, int framesStart, int offsetStart, int kStop, int framesStop, int offsetStop){
type=type_;
name=ProkObject.typeStrings[type];
setInner(kInner, framesInner);
setStart(kStart, framesStart, offsetStart);
setStop(kStop, framesStop, offsetStop);
}
StatsContainer(int type_){
type=type_;
name=ProkObject.typeStrings[type];
}
void setInner(int kInner, int framesInner){
assert(inner==null);
statsArray[0]=inner=new FrameStats(name+" inner", kInner, framesInner, 0);
}
void setStart(int kStart, int framesStart, int offsetStart){
assert(start==null);
statsArray[1]=start=new FrameStats(name+" start", kStart, framesStart, offsetStart);
}
void setStop(int kStop, int framesStop, int offsetStop){
assert(stop==null);
statsArray[2]=stop=new FrameStats(name+" stop", kStop, framesStop, offsetStop);
}
void setInner(FrameStats fs){
assert(inner==null);
assert(fs!=null);
statsArray[0]=inner=fs;
}
void setStart(FrameStats fs){
assert(start==null);
statsArray[1]=start=fs;
}
void setStop(FrameStats fs){
assert(stop==null);
statsArray[2]=stop=fs;
}
/*--------------------------------------------------------------*/
/*---------------- Methods ----------------*/
/*--------------------------------------------------------------*/
@Override
public String toString(){
return appendTo(new ByteBuilder()).toString();
}
public ByteBuilder appendTo(ByteBuilder bb) {
bb.append("#name\t").append(name).nl();
bb.append("#type\t").append(type).nl();
bb.append("#count\t").append(lengthCount).nl();
bb.append("#lengthSum\t").append(lengthSum).nl();
//lengths
bb.append("#contains\t").append(3).nl();
if(ProkObject.processType(type)) {
for(FrameStats fs : statsArray){
fs.appendTo(bb);
}
}else{
for(FrameStats fs : statsArray){
fs.append0(bb);
}
}
return bb;
}
public void clear(){
for(int i=0; i<statsArray.length; i++){
if(statsArray[i]!=null){
statsArray[i].clear();
}
}
assert(inner==statsArray[0]);
assert(start==statsArray[1]);
assert(stop==statsArray[2]);
Arrays.fill(lengths, 0);
lengthSum=0;
lengthCount=0;
calculate();
}
public void setFrom(StatsContainer sc){
assert(sc.name.equals(name));
for(int i=0; i<statsArray.length; i++){
FrameStats fs=sc.statsArray[i];
if(statsArray[i]==null){
statsArray[i]=new FrameStats(fs.name, fs.k, fs.frames, fs.leftOffset);
statsArray[i].add(fs);
}else{
statsArray[i].setFrom(fs);
}
}
inner=statsArray[0];
start=statsArray[1];
stop=statsArray[2];
for(int i=0; i<lengths.length; i++){lengths[i]=sc.lengths[i];}
lengthSum=sc.lengthSum;
lengthCount=sc.lengthCount;
calculate();
}
public void add(StatsContainer sc){
assert(sc.name.equals(name));
for(int i=0; i<statsArray.length; i++){
FrameStats fs=sc.statsArray[i];
if(statsArray[i]==null){
statsArray[i]=new FrameStats(fs.name, fs.k, fs.frames, fs.leftOffset);
}
statsArray[i].add(fs);
}
inner=statsArray[0];
start=statsArray[1];
stop=statsArray[2];
Tools.add(lengths, sc.lengths);
lengthSum+=sc.lengthSum;
lengthCount+=sc.lengthCount;
calculate();
}
public void multiplyBy(double mult) {
for(int i=0; i<statsArray.length; i++){
FrameStats fs=statsArray[i];
fs.multiplyBy(mult);
}
Tools.multiplyBy(lengths, mult);
lengthSum=Math.round(lengthSum*mult);
lengthCount=Math.round(lengthCount*mult);
calculate();
}
public void calculate(){
for(int i=0; i<statsArray.length; i++){
statsArray[i].calculate();
}
lengthAvg=(int)(lengthSum/Tools.max(1.0, lengthCount));
invLengthAvg=1f/Tools.max(1, lengthAvg);
}
public void addLength(int x){
lengthSum+=x;
lengthCount++;
lengths[Tools.min(x, lengths.length-1)]++;
}
/*--------------------------------------------------------------*/
/*---------------- Fields ----------------*/
/*--------------------------------------------------------------*/
FrameStats inner;
FrameStats start;
FrameStats stop;
final FrameStats[] statsArray=new FrameStats[3];
int kLongLen(){return ProkObject.kLongLen(type);}
LongHashSet kmerSet(){return ProkObject.kmerSet(type);}
Read[] consensusSequence(){return ProkObject.consensusReads(type);}
float minIdentity(){return ProkObject.minID(type);}
public int startSlop(){return ProkObject.startSlop(type);}
public int stopSlop(){return ProkObject.stopSlop(type);}
final String name;
long lengthSum=0;
long lengthCount=0;
int lengthAvg=-1;
float invLengthAvg;
int[] lengths=new int[5000];
public final int type;
}
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