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Copy pathConversionGraphStatsLogger.java
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255 lines (216 loc) · 7.78 KB
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/*
* Copyright (C) 2013 Tim Vaughan <tgvaughan@gmail.com>
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package bacter.util;
import bacter.Conversion;
import bacter.ConversionGraph;
import bacter.Locus;
import bacter.Region;
import beast.base.inference.CalculationNode;
import beast.base.core.Input;
import beast.base.core.Input.Validate;
import beast.base.core.Loggable;
import beast.base.util.Randomizer;
import java.io.PrintStream;
/**
*
* @author Tim Vaughan <tgvaughan@gmail.com>
*/
public class ConversionGraphStatsLogger extends CalculationNode implements Loggable {
public Input<ConversionGraph> acgInput = new Input <>(
"acg", "Conversion graph to calculate summary statistics from.",
Validate.REQUIRED);
private ConversionGraph acg;
@Override
public void initAndValidate() {
acg = acgInput.get();
}
/**
* Obtain mean length of converted regions described by ACG.
*
* @param acg
* @param locus
* @return mean length, or NaN if ACG has no converted edges.
*/
public static double getMeanTractLength(ConversionGraph acg, Locus locus) {
if (acg.getConvCount(locus)<1)
return Double.NaN;
double mean = 0;
for (Conversion conv : acg.getConversions(locus))
mean += conv.getEndSite()-conv.getStartSite()+1;
mean /= acg.getConvCount(locus);
return mean;
}
/**
* Obtain mean length of contiguous regions having the same marginal
* tree and being affected by at least 1 conversion.
*
* @param acg
* @param locus
* @return mean length
*/
public static double getMeanRegionLength(ConversionGraph acg, Locus locus) {
double sum = 0.0;
int count = 0;
for (Region region : acg.getRegions(locus))
if (!region.isClonalFrame()) {
sum += region.getRegionLength();
count += 1;
}
if (count == 0)
return Double.NaN;
else
return sum/count;
}
/**
* Obtain average position of conversion startSites.
*
* @param acg
* @param locus
* @return average site index or NaN if no conversions in ACG.
*/
public static double getMeanStartSite(ConversionGraph acg, Locus locus) {
if (acg.getConvCount(locus)<1)
return Double.NaN;
double mean = 0.0;
for (Conversion conv : acg.getConversions(locus))
mean += conv.getStartSite();
mean /= acg.getConvCount(locus);
return mean;
}
/**
* Retrieve end site of randomly chosen conversion in ACG. Used for
* assessing end site distribution.
*
* @param acg
* @param locus
* @return end site index or NaN if no conversions
*/
public static double getRandomEndSite(ConversionGraph acg, Locus locus) {
if (acg.getConvCount(locus)<1)
return Double.NaN;
else
return acg.getConversions(locus).get(
Randomizer.nextInt(acg.getConvCount(locus))).getEndSite();
}
/**
* Retrieve starting site of randomly chosen conversion in ACG. Used for
* assessing start site distribution.
*
* @param acg
* @param locus
* @return start site index or NaN if no conversions
*/
public static double getRandomStartSite(ConversionGraph acg, Locus locus) {
if (acg.getConvCount(locus)<1)
return Double.NaN;
else
return acg.getConversions(locus).get(
Randomizer.nextInt(acg.getConvCount(locus))).getStartSite();
}
/**
* Obtain average position of conversion ends.
*
* @param acg
* @param locus
* @return average site index or NaN if no conversions in ACG.
*/
public static double getMeanEndSite(ConversionGraph acg, Locus locus) {
if (acg.getConvCount(locus)<1)
return Double.NaN;
double mean = 0.0;
for (Conversion conv : acg.getConversions(locus))
mean += conv.getEndSite();
mean /= acg.getConvCount(locus);
return mean;
}
/**
* Obtain mean length of converted edges in ACG.
*
* @param acg
* @return mean length, or NaN if ACG has no converted edges
*/
public static double getMeanEdgeLength(ConversionGraph acg) {
if (acg.getTotalConvCount()<1)
return Double.NaN;
double mean = 0.0;
for (Locus locus : acg.getConvertibleLoci()) {
for (Conversion conv : acg.getConversions(locus))
mean += conv.getHeight2() - conv.getHeight1();
}
mean /= acg.getTotalConvCount();
return mean;
}
/**
* Obtain mean height of point of departure of converted edges
* in ACG.
*
* @param acg
* @return mean height, or NaN if ACG has no converted edges
*/
public static double getMeanDepartureHeight(ConversionGraph acg) {
if (acg.getTotalConvCount()<1)
return Double.NaN;
double mean = 0.0;
for (Locus locus : acg.getConvertibleLoci()) {
for (Conversion conv : acg.getConversions(locus)) {
mean += conv.getHeight1();
}
}
mean /= acg.getTotalConvCount();
return mean;
}
@Override
public void init(PrintStream out) {
String id = acg.getID();
if (id == null || id.matches("\\s*"))
id = "acg";
out.print(id + ".CFheight\t"
+ id + ".CFlength\t"
+ id + ".nConv\t"
+ id + ".nUselessConvs\t"
+ id + ".meanEdgeLength\t"
+ id + ".meanDepartureHeight\t");
for (Locus loci : acg.getConvertibleLoci()) {
String lid = id + "." + loci.getID();
out.print(lid + ".meanTractLength\t"
+ lid + ".meanRegionLength\t"
+ lid + ".meanStartSite\t"
+ lid + ".meanEndSite\t"
+ lid + ".randomStartSite\t"
+ lid + ".randomEndSite\t");
}
}
@Override
public void log(long nSample, PrintStream out) {
out.print(acg.getRoot().getHeight() + "\t"
+ acg.getClonalFrameLength() + "\t"
+ acg.getTotalConvCount() + "\t"
+ acg.getUselessConvCount() + "\t"
+ ConversionGraphStatsLogger.getMeanEdgeLength(acg) + "\t"
+ ConversionGraphStatsLogger.getMeanDepartureHeight(acg) + "\t");
for (Locus locus : acg.getConvertibleLoci()) {
out.print(ConversionGraphStatsLogger.getMeanTractLength(acg, locus) + "\t"
+ ConversionGraphStatsLogger.getMeanRegionLength(acg, locus) + "\t"
+ ConversionGraphStatsLogger.getMeanStartSite(acg, locus) + "\t"
+ ConversionGraphStatsLogger.getMeanEndSite(acg, locus) + "\t"
+ ConversionGraphStatsLogger.getRandomStartSite(acg, locus) + "\t"
+ ConversionGraphStatsLogger.getRandomEndSite(acg, locus) + "\t");
}
}
@Override
public void close(PrintStream out) { }
}