--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/java-genomics-toolkit/src/edu/unc/genomics/visualization/MatrixAligner.java	Mon Feb 13 21:55:55 2012 -0500
@@ -0,0 +1,145 @@
+package edu.unc.genomics.visualization;
+
+import java.io.BufferedWriter;
+import java.io.IOException;
+import java.nio.charset.Charset;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.Arrays;
+import java.util.Iterator;
+import java.util.List;
+
+import org.apache.commons.lang3.ArrayUtils;
+import org.apache.log4j.Logger;
+import org.broad.igv.bbfile.WigItem;
+
+import com.beust.jcommander.Parameter;
+
+import edu.unc.genomics.BedEntry;
+import edu.unc.genomics.CommandLineTool;
+import edu.unc.genomics.ReadablePathValidator;
+import edu.unc.genomics.io.BedFile;
+import edu.unc.genomics.io.WigFile;
+import edu.unc.genomics.io.WigFileException;
+
+public class MatrixAligner extends CommandLineTool {
+
+	private static final Logger log = Logger.getLogger(MatrixAligner.class);
+
+	@Parameter(names = {"-i", "--input"}, description = "Input file (Wig)", required = true)
+	public WigFile inputFile;
+	@Parameter(names = {"-l", "--loci"}, description = "Loci file (Bed)", required = true, validateWith = ReadablePathValidator.class)
+	public Path lociFile;
+	@Parameter(names = {"-m", "--max"}, description = "Truncate width (base pairs)")
+	public Integer maxWidth;
+	@Parameter(names = {"-o", "--output"}, description = "Output file (matrix2png format)", required = true)
+	public Path outputFile;
+	
+	private List<BedEntry> loci;
+	
+	@Override
+	public void run() throws IOException {		
+		log.debug("Loading alignment intervals");
+		try (BedFile bed = new BedFile(lociFile)) {
+			loci = bed.loadAll();
+		}
+		
+		// Compute the matrix dimensions
+		int leftMax = Integer.MIN_VALUE;
+		int rightMax = Integer.MIN_VALUE;
+		for (BedEntry entry : loci) {
+			int left = Math.abs(entry.getValue().intValue()-entry.getStart());
+			int right = Math.abs(entry.getValue().intValue()-entry.getStop());
+			if (left > leftMax) {
+				leftMax = left;
+			}
+			if (right > rightMax) {
+				rightMax = right;
+			}
+		}
+		
+		int m = loci.size();
+		int n = leftMax + rightMax + 1;
+		int alignmentPoint = leftMax;
+		log.info("Intervals aligned into: " + m+"x"+n + " matrix");
+		log.info("Alignment point: " + alignmentPoint);
+		
+		int leftBound = 0;
+		int rightBound = n-1;
+		if (maxWidth != null && maxWidth < n) {
+			log.info("Truncated to: " + m+"x"+maxWidth);
+			int leftAlignDistance = alignmentPoint;
+			int rightAlignDistance = n - alignmentPoint - 1;
+			int halfMax = maxWidth / 2;
+			
+			if (halfMax < leftAlignDistance && halfMax < rightAlignDistance) {
+				leftBound = alignmentPoint - halfMax;
+				rightBound = alignmentPoint + halfMax;
+			} else {
+				if (leftAlignDistance <= rightAlignDistance) {
+					rightBound = maxWidth;
+				} else {
+					leftBound = n - maxWidth;
+				}
+			}
+		}
+		
+		log.debug("Initializing output file");
+		int count = 0, skipped = 0;
+		try (BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) {
+			writer.write("ID");
+			for (int i = leftBound-alignmentPoint; i <= rightBound-alignmentPoint; i++) {
+				writer.write("\t"+i);
+			}
+			writer.newLine();
+			
+			log.debug("Iterating over all intervals");
+			String[] row = new String[n];
+			for (BedEntry entry : loci) {
+				Iterator<WigItem> result = null;
+				try {
+					result = inputFile.query(entry);
+				} catch (WigFileException e) {
+					skipped++;
+					continue;
+				}
+				
+				float[] data = WigFile.flattenData(result, entry.getStart(), entry.getStop());
+				// Reverse if on the crick strand
+				if (entry.isCrick()) {
+					ArrayUtils.reverse(data);
+				}
+				
+				// Position the data in the matrix
+				// Locus alignment point (entry value) should be positioned over the matrix alignment point
+				int n1 = alignmentPoint - Math.abs(entry.getValue().intValue()-entry.getStart());
+				int n2 = alignmentPoint + Math.abs(entry.getValue().intValue()-entry.getStop());
+				assert data.length == n2-n1+1;
+				
+				Arrays.fill(row, "-");
+				for (int i = 0; i < data.length; i++) {
+					if (!Float.isNaN(data[i])) {
+						row[n1+i] = String.valueOf(data[i]);
+					}
+				}
+				
+				// Write to output
+				String id = ((entry.getId() == null) ? entry.getId() : "Row "+(count++));
+				writer.write(id);
+				for (int i = leftBound; i <= rightBound; i++) {
+					writer.write("\t"+row[i]);
+				}
+				writer.newLine();
+			}
+		}
+		
+		inputFile.close();
+		log.info(count + " intervals processed");
+		log.info(skipped + " intervals skipped");
+	}
+	
+	public static void main(String[] args) {
+		new MatrixAligner().instanceMain(args);
+	}
+
+}