/*
* Copyright (c) 2007-2011 by The Broad Institute of MIT and Harvard. All Rights Reserved.
*
* This software is licensed under the terms of the GNU Lesser General Public License (LGPL),
* Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.
*
* THE SOFTWARE IS PROVIDED "AS IS." THE BROAD AND MIT MAKE NO REPRESENTATIONS OR
* WARRANTES OF ANY KIND CONCERNING THE SOFTWARE, EXPRESS OR IMPLIED, INCLUDING,
* WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
* PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER
* OR NOT DISCOVERABLE. IN NO EVENT SHALL THE BROAD OR MIT, OR THEIR RESPECTIVE
* TRUSTEES, DIRECTORS, OFFICERS, EMPLOYEES, AND AFFILIATES BE LIABLE FOR ANY DAMAGES
* OF ANY KIND, INCLUDING, WITHOUT LIMITATION, INCIDENTAL OR CONSEQUENTIAL DAMAGES,
* ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER
* THE BROAD OR MIT SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT
* SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
*/
package org.broad.igv.synteny;
import org.broad.igv.data.DataUtils;
import org.broad.igv.data.WiggleDataset;
import org.broad.igv.data.WiggleParser;
import org.broad.igv.feature.FeatureUtils;
import org.broad.igv.feature.LocusScore;
import org.broad.igv.track.WindowFunction;
import org.broad.igv.util.ResourceLocator;
import java.io.File;
import java.io.FileWriter;
import java.io.PrintWriter;
import java.util.ArrayList;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
/**
* @author jrobinso
*/
public class BlastMappingUtils {
/**
* Method description
*
* @param dataset
* @param mappings
* @param outputFile
*/
public static void MapWigFile(WiggleDataset dataset, List<BlastMapping> mappings, File outputFile) {
PrintWriter pw = null;
try {
pw = new PrintWriter(new FileWriter(outputFile));
// Segregate and sort ortholog
Map<String, List<BlastMapping>> featureMap = new LinkedHashMap();
for (BlastMapping f : mappings) {
List<BlastMapping> fList = featureMap.get(f.getChr());
if (fList == null) {
fList = new ArrayList();
featureMap.put(f.getChr(), fList);
}
fList.add(f);
}
for (List<BlastMapping> featureList : featureMap.values()) {
FeatureUtils.sortFeatureList(featureList);
}
pw.println("Chr\tStart\tEnd\t\tnucCount (Kwal)");
// Loop through chromosomes
for (String chr : featureMap.keySet()) {
List<BlastMapping> mappingList = featureMap.get(chr);
List<BasicScore> scores = new ArrayList(mappingList.size());
for (BlastMapping mapping : mappingList) {
BlastMapping.Block queryBlock = mapping.getQueryBlock();
BlastMapping.Block subjectBlock = mapping.getSubjectBlock();
int[] subjectPosition = dataset.getStartLocations(subjectBlock.getContig());
float[] data = dataset.getData("ignore", subjectBlock.getContig());
int s0 = subjectBlock.getStart();
int s1 = subjectBlock.getEnd();
int q0 = queryBlock.getStart();
int q1 = queryBlock.getEnd();
int idx0 = DataUtils.getIndexBefore(subjectPosition, Math.min(s0, s1));
int idx1 = DataUtils.getIndexBefore(subjectPosition, Math.max(s0, s1)) + 1;
if (idx1 == subjectPosition.length) {
idx1--;
}
double beta = ((double) (q1 - q0)) / (s1 - s0);
for (int i = idx0; i <= idx1; i++) {
int pos = (int) (q0 + beta * (subjectPosition[i] - s0));
float d = data[i];
scores.add(new BasicScore(chr, pos, pos + 1, d));
}
}
FeatureUtils.sortFeatureList(scores);
for (BasicScore s : scores) {
pw.println(s.getChr() + "\t" + s.getStart() + "\t" +
(s.getEnd() + 1) + "\t\t" + s.getScore());
}
}
}
catch (Exception e) {
e.printStackTrace();
}
finally {
pw.close();
}
}
static class BasicScore implements LocusScore {
String chr;
int start;
int end;
float score;
public BasicScore(String chromosome, int start, int end, float score) {
this.chr = chromosome;
this.start = start;
this.end = end;
this.score = score;
}
public BasicScore(BasicScore bs) {
this.chr = bs.chr;
this.start = bs.start;
this.end = bs.end;
this.score = bs.score;
}
public BasicScore copy() {
return new BasicScore(this);
}
public String getChr() {
return chr;
}
public int getStart() {
return start;
}
public float getScore() {
return score;
}
public void setStart(int start) {
this.start = start;
}
public int getEnd() {
return end;
}
public void setEnd(int end) {
this.end = end;
}
public String getValueString(double position, WindowFunction windowFunction) {
return "Value: " + score;
//throw new UnsupportedOperationException("Not supported yet.");
}
public int getExtendedStart() {
return getStart();
}
public int getExtendedEnd() {
return getEnd();
}
}
}