org.snpeff.outputFormatter.OutputFormatter Maven / Gradle / Ivy

Go to download
Show more of this group Show more artifacts with this name
Show all versions of SnpEff Show documentation
Variant annotation and effect prediction package.
The newest version!
package org.snpeff.outputFormatter;

import java.io.BufferedWriter;
import java.io.FileWriter;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;

import org.snpeff.filter.VariantEffectFilter;
import org.snpeff.interval.Marker;
import org.snpeff.snpEffect.Config;
import org.snpeff.snpEffect.VariantEffect;

/**
 * Formats output
 * How is this used:
 *    - newSection();   // Create a new 'section' on the output format (e.g. a new seqChange)
 *    - add();			// Add all changes related to this section (i.e. all changes related to this seqChange)
 *    - endSection();	// Output all changes related to this section (output header if needed), clean up list of changes
 *
 * @author pcingola
 */
public abstract class OutputFormatter {

	boolean supressOutput = false; // Do not print anything (used for testCases)
	boolean showHeader = true; // Show header information
	boolean useHgvs; // Use HGVS notation
	boolean useGeneId; // Use Gene ID instead of gene name
	boolean useSequenceOntology; // Use Sequence Ontology terms
	boolean useOicr; // Use OICR tag
	int sectionNum = 0;
	int outOffset = 1;
	String commandLineStr;
	String version;
	String chrStr;
	String outputFile = null;
	BufferedWriter out;
	Marker section;
	VariantEffectFilter variantEffectResutFilter = null; // Filter prediction results
	List variantEffects;
	Config config;

	public OutputFormatter() {
		variantEffects = new ArrayList();
	}

	public void setOutputWriter(BufferedWriter out) {
		this.out = out;
	}


	/**
	 * Add effects to list
	 */
	public void add(VariantEffect variantEffect) {
		// Passes the filter? => Add
		if ((variantEffectResutFilter == null) || (!variantEffectResutFilter.filter(variantEffect))) variantEffects.add(variantEffect);
	}

	@Override
	public OutputFormatter clone() {
		OutputFormatter newOutputFormatter = null;
		try {
			// Create a new formatter. We cannot use the same output formatter for all workers
			newOutputFormatter = this.getClass().newInstance();
			newOutputFormatter.supressOutput = supressOutput;
			newOutputFormatter.showHeader = showHeader;
			newOutputFormatter.useHgvs = useHgvs;
			newOutputFormatter.useGeneId = useGeneId;
			newOutputFormatter.useSequenceOntology = useSequenceOntology;
			newOutputFormatter.useOicr = useOicr;
			newOutputFormatter.sectionNum = sectionNum;
			newOutputFormatter.outOffset = outOffset;
			newOutputFormatter.commandLineStr = commandLineStr;
			newOutputFormatter.version = version;
			newOutputFormatter.chrStr = chrStr;
			newOutputFormatter.section = section;
			newOutputFormatter.variantEffectResutFilter = variantEffectResutFilter;
			newOutputFormatter.config = config;

		} catch (Exception e) {
			throw new RuntimeException(e);
		}

		return newOutputFormatter;
	}

	/**
	 * CLose output files, if any
	 */
	public void close() {
		if (out != null) {
			try {
				out.close();
			} catch (IOException e) {
				throw new RuntimeException(e);
			}
		}
	}

	/**
	 * Finish up section
	 */
	public String endSection(Marker marker) {
		StringBuilder sb = new StringBuilder();

		// Add header?
		if (showHeader && (sectionNum == 0)) {
			String header = toStringHeader();
			if (!header.isEmpty()) {
				sb.append(header);
				sb.append("\n");
			}
		}

		// Add current line
		sb.append(toString());

		sectionNum++;
		variantEffects.clear();

		return supressOutput ? null : sb.toString();
	}

	/**
	 * Print a "raw" string to a file
	 */
	public void print(String outStr) {
		try {
			// Open output file?
			if ((outputFile != null) && (out == null)) out = new BufferedWriter(new FileWriter(outputFile));

			// Write something?
			if ((outStr != null) && (!outStr.isEmpty())) {
				// Write to file?
				if (out != null) {
					out.write(outStr);
					out.write("\n");
				} else if (!supressOutput) System.out.println(outStr); // Show on STDOUT
			}
		} catch (IOException e) {
			throw new RuntimeException(e);
		}
	}

	/**
	 * End this section and print results
	 */
	public void printSection(Marker marker) {
		print(endSection(marker));
	}

	public void setChrStr(String chrStr) {
		this.chrStr = chrStr;
	}

	public void setCommandLineStr(String commandLineStr) {
		this.commandLineStr = commandLineStr;
	}

	public void setConfig(Config config) {
		this.config = config;
	}

	public void setOutOffset(int outOffset) {
		this.outOffset = outOffset;
	}

	public void setOutputFile(String outputFile) {
		this.outputFile = outputFile;
	}

	public void setShowHeader(boolean showHeader) {
		this.showHeader = showHeader;
	}

	public void setSupressOutput(boolean supressOutput) {
		this.supressOutput = supressOutput;
	}

	public void setUseGeneId(boolean useGeneId) {
		this.useGeneId = useGeneId;
	}

	public void setUseHgvs(boolean useHgvs) {
		this.useHgvs = useHgvs;
	}

	public void setUseOicr(boolean useOicr) {
		this.useOicr = useOicr;
	}

	public void setUseSequenceOntology(boolean useSequenceOntology) {
		this.useSequenceOntology = useSequenceOntology;
	}

	public void setVariantEffectResutFilter(VariantEffectFilter changeEffectResutFilter) {
		variantEffectResutFilter = changeEffectResutFilter;
	}

	public void setVersion(String version) {
		this.version = version;
	}

	/**
	 * Starts a new section
	 */
	public void startSection(Marker marker) {
		section = marker;
	}

	@Override
	public String toString() {
		throw new RuntimeException("Method toString() must be overridden!");
	}

	/**
	 * Show header
	 */
	protected abstract String toStringHeader();
}