From ade1971581f9b72bb9d467f104c04c8a08a200e0 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Tue, 20 Mar 2012 00:12:17 -0400 Subject: [PATCH] Since we allow any generic header types, there's no longer any reason to check for supported types --- .../utils/codecs/vcf/AbstractVCFCodec.java | 4 +-- .../utils/codecs/vcf/VCFFilterHeaderLine.java | 4 +-- .../utils/codecs/vcf/VCFSimpleHeaderLine.java | 32 ++++++------------- 3 files changed, 14 insertions(+), 26 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java index 273d5a377..8180eba30 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java @@ -167,10 +167,10 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec { metaData.add(format); formatFields.put(format.getID(), format.getType()); } else if ( str.startsWith(VCFConstants.CONTIG_HEADER_START) ) { - final VCFSimpleHeaderLine contig = new VCFSimpleHeaderLine(str.substring(9), version, VCFSimpleHeaderLine.SupportedHeaderLineType.GENERIC, null); + final VCFSimpleHeaderLine contig = new VCFSimpleHeaderLine(str.substring(9), version, VCFConstants.CONTIG_HEADER_START.substring(2), null); metaData.add(contig); } else if ( str.startsWith(VCFConstants.ALT_HEADER_START) ) { - final VCFSimpleHeaderLine alt = new VCFSimpleHeaderLine(str.substring(6), version, VCFSimpleHeaderLine.SupportedHeaderLineType.GENERIC, Arrays.asList("ID", "Description")); + final VCFSimpleHeaderLine alt = new VCFSimpleHeaderLine(str.substring(6), version, VCFConstants.ALT_HEADER_START.substring(2), Arrays.asList("ID", "Description")); metaData.add(alt); } else { int equals = str.indexOf("="); diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFilterHeaderLine.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFilterHeaderLine.java index 72504abd5..dd0a333f3 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFilterHeaderLine.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFilterHeaderLine.java @@ -15,7 +15,7 @@ public class VCFFilterHeaderLine extends VCFSimpleHeaderLine { * @param description the description for this header line */ public VCFFilterHeaderLine(String name, String description) { - super(name, description, SupportedHeaderLineType.FILTER); + super("FILTER", name, description); } /** @@ -25,6 +25,6 @@ public class VCFFilterHeaderLine extends VCFSimpleHeaderLine { * @param version the vcf header version */ protected VCFFilterHeaderLine(String line, VCFHeaderVersion version) { - super(line, version, SupportedHeaderLineType.FILTER, Arrays.asList("ID", "Description")); + super(line, version, "FILTER", Arrays.asList("ID", "Description")); } } \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFSimpleHeaderLine.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFSimpleHeaderLine.java index ea485e956..05d603073 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFSimpleHeaderLine.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFSimpleHeaderLine.java @@ -11,41 +11,30 @@ import java.util.Map; */ public class VCFSimpleHeaderLine extends VCFHeaderLine implements VCFIDHeaderLine { - public enum SupportedHeaderLineType { - FILTER, GENERIC; - } - private String name; private Map genericFields = new LinkedHashMap(); - - // our type of line, i.e. filter, alt, etc - private final SupportedHeaderLineType lineType; - - /** * create a VCF filter header line * + * @param key the key for this header line * @param name the name for this header line * @param genericFields other fields for this header line - * @param lineType the header line type */ - public VCFSimpleHeaderLine(String name, Map genericFields, SupportedHeaderLineType lineType) { - super(lineType.toString(), ""); - this.lineType = lineType; + public VCFSimpleHeaderLine(String key, String name, Map genericFields) { + super(key, ""); initialize(name, genericFields); } /** * create a VCF filter header line * + * @param key the key for this header line * @param name the name for this header line * @param description description for this header line - * @param lineType the header line type */ - public VCFSimpleHeaderLine(String name, String description, SupportedHeaderLineType lineType) { - super(lineType.toString(), ""); - this.lineType = lineType; + public VCFSimpleHeaderLine(String key, String name, String description) { + super(key, ""); Map map = new LinkedHashMap(1); map.put("Description", description); initialize(name, map); @@ -56,12 +45,11 @@ public class VCFSimpleHeaderLine extends VCFHeaderLine implements VCFIDHeaderLin * * @param line the header line * @param version the vcf header version - * @param lineType the header line type + * @param key the key for this header line * @param expectedTagOrdering the tag ordering expected for this header line */ - protected VCFSimpleHeaderLine(String line, VCFHeaderVersion version, SupportedHeaderLineType lineType, List expectedTagOrdering) { - super(lineType.toString(), ""); - this.lineType = lineType; + protected VCFSimpleHeaderLine(String line, VCFHeaderVersion version, String key, List expectedTagOrdering) { + super(key, ""); Map mapping = VCFHeaderLineTranslator.parseLine(version, line, expectedTagOrdering); name = mapping.get("ID"); initialize(name, mapping); @@ -79,7 +67,7 @@ public class VCFSimpleHeaderLine extends VCFHeaderLine implements VCFIDHeaderLin Map map = new LinkedHashMap(); map.put("ID", name); map.putAll(genericFields); - return lineType.toString() + "=" + VCFHeaderLine.toStringEncoding(map); + return getKey() + "=" + VCFHeaderLine.toStringEncoding(map); } public boolean equals(Object o) {