org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature Maven / Gradle / Ivy
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package org.broadinstitute.hellbender.utils.codecs.gtf;
import com.google.common.annotations.VisibleForTesting;
import htsjdk.samtools.util.Locatable;
import htsjdk.tribble.Feature;
import htsjdk.tribble.annotation.Strand;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.broadinstitute.hellbender.exceptions.UserException;
import org.broadinstitute.hellbender.utils.SimpleInterval;
import org.broadinstitute.hellbender.utils.Utils;
import java.util.*;
import java.util.regex.Pattern;
import java.util.stream.Collectors;
/**
* A {@link GencodeGtfFeature} represents data in a GENCODE GTF file.
*
* Features are grouped logically by related data.
* While the abstract class {@link GencodeGtfFeature} represents a single line
* of a GENCODE GTF File, the concrete instantiations represent at least one line,
* and often more than one.
*
* For example, a {@link GencodeGtfGeneFeature} represents all lines in the given
* data file with information on a particular gene. This includes all transcripts,
* exons, coding regions, etc. in that gene.
*
* Similarly, a {@link GencodeGtfTranscriptFeature} represents all lines in the given
* data file with information on a particular transcript.
*
* However, a {@link GencodeGtfSelenocysteineFeature} represents a particular line
* in the given data file that contains information on a specific selenocysteine.
*
* The specification of a GTF file is defined here:
* http://mblab.wustl.edu/GTF22.html
*
* Currently only supports GENCODE versions 19-26.
*
* Created by jonn on 7/21/17.
*/
public abstract class GencodeGtfFeature implements Feature, Comparable {
private static final Logger logger = LogManager.getLogger(GencodeGtfFeature.class);
// ===========================================================================
public static final String ANNOTATION_SOURCE_ENSEMBL = "ENSEMBL";
public static final String ANNOTATION_SOURCE_HAVANA = "HAVANA";
public static final String ANNOTATION_SOURCE_ENA = "ena";
// ===========================================================================
// Metadata fields:
private static final String FIELD_DELIMITER = "\t";
public static final int NO_FEATURE_ORDER = -1;
public static final int NO_EXON_NUMBER = -1;
private static final int NUM_FIELDS = 9;
private static final int CHROMOSOME_NAME_INDEX = 0;
private static final int ANNOTATION_SOURCE_INDEX = 1;
private static final int FEATURE_TYPE_INDEX = 2;
private static final int START_LOCATION_INDEX = 3;
private static final int END_LOCATION_INDEX = 4;
private static final int GENOMIC_STRAND_INDEX = 6;
private static final int GENOMIC_PHASE_INDEX = 7;
private static final int EXTRA_FIELDS_INDEX = 8;
private static final String EXTRA_FIELD_DELIMITER = ";";
private static final int EXTRA_FIELD_KEY_INDEX = 0;
private static final int EXTRA_FIELD_VALUE_INDEX = 1;
public static final String EXTRA_FIELD_KEY_VALUE_SPLITTER = " ";
private static final Pattern NUMBER_PATTERN = Pattern.compile("\\d\\d*");
private String ucscGenomeVersion = null;
@VisibleForTesting
final GencodeGtfFeatureBaseData baseData;
// ================================================================================================
/**
* Populate this GencodeGtfFeature with the given data.
* @param gtfFields {@link String[]} containing an ordered list of fields to use to populate this {@link GencodeGtfFeature}.
* @param gtfFileType A {@link String} containing the file type of the GTF data that created this {@link GencodeGtfFeature}.
*/
protected GencodeGtfFeature(final String[] gtfFields, final String gtfFileType) {
Utils.validateArg(gtfFields.length == NUM_FIELDS, "Unexpected number of fields: " + gtfFields.length + " != " + NUM_FIELDS);
baseData = new GencodeGtfFeatureBaseData();
try {
baseData.genomicPosition = new SimpleInterval(
gtfFields[CHROMOSOME_NAME_INDEX],
Integer.valueOf(gtfFields[START_LOCATION_INDEX]),
Integer.valueOf(gtfFields[END_LOCATION_INDEX])
);
}
catch (final NumberFormatException ex) {
throw new UserException.MalformedFile("Cannot read integer value for start/end position!");
}
baseData.gtfSourceFileType = gtfFileType;
baseData.annotationSource = gtfFields[ANNOTATION_SOURCE_INDEX];
baseData.featureType = GencodeGtfFeature.FeatureType.getEnum( gtfFields[FEATURE_TYPE_INDEX].toLowerCase() );
baseData.genomicStrand = convertStringToStrand( gtfFields[GENOMIC_STRAND_INDEX] );
baseData.genomicPhase = GenomicPhase.getEnum( gtfFields[GENOMIC_PHASE_INDEX] );
// Get the extra fields from the last column:
final String[] extraFields = gtfFields[EXTRA_FIELDS_INDEX].split(EXTRA_FIELD_DELIMITER, -1);
final StringBuilder anonymousOptionalFieldBuilder = new StringBuilder();
// Now there are "optional" fields to go through (some actually required, some actually optional),
// But we need to match up the field names to the fields themselves:
for ( final String extraField : extraFields ) {
final String trimmedExtraField = extraField.trim();
if (trimmedExtraField.isEmpty()) {
continue;
}
final int splitPoint = trimmedExtraField.indexOf(EXTRA_FIELD_KEY_VALUE_SPLITTER);
if( splitPoint == -1 ) {
throw new UserException.MalformedFile("Extraneous optional field data - not in a key/value pair: " + extraField);
}
final String fieldName = trimmedExtraField.substring(0, splitPoint).trim();
// The value of the field may be between two quotes.
// We remove them here.
final String rawFieldValue = trimmedExtraField.substring(splitPoint + 1, trimmedExtraField.length());
final String fieldValue = StringUtils.remove(rawFieldValue.trim(), '"');
if( fieldValue.contains(EXTRA_FIELD_KEY_VALUE_SPLITTER) ){
throw new UserException("Expected a key/value pair but found several values " + fieldName + "/" + fieldValue);
}
OptionalField optionalField = null;
switch (fieldName) {
// Find the right field to set:
case GencodeGTFFieldConstants.GENE_ID:
baseData.geneId = fieldValue;
break;
case GencodeGTFFieldConstants.TRANSCRIPT_ID:
baseData.transcriptId = fieldValue;
break;
case GencodeGTFFieldConstants.GENE_TYPE:
baseData.geneType = fieldValue;
break;
// For ENSEMBL GTF files:
case GencodeGTFFieldConstants.GENE_BIOTYPE:
baseData.geneType = fieldValue;
break;
case GencodeGTFFieldConstants.GENE_STATUS:
baseData.geneStatus = fieldValue;
break;
case GencodeGTFFieldConstants.GENE_NAME:
baseData.geneName = fieldValue;
break;
case GencodeGTFFieldConstants.TRANSCRIPT_TYPE:
baseData.transcriptType = fieldValue;
break;
case GencodeGTFFieldConstants.TRANSCRIPT_BIOTYPE:
baseData.transcriptType = fieldValue;
break;
case GencodeGTFFieldConstants.TRANSCRIPT_STATUS:
baseData.transcriptStatus = fieldValue;
break;
case GencodeGTFFieldConstants.TRANSCRIPT_NAME:
baseData.transcriptName = fieldValue;
break;
case GencodeGTFFieldConstants.EXON_NUMBER:
try {
baseData.exonNumber = Integer.valueOf(fieldValue);
}
catch (final NumberFormatException ex) {
throw new UserException.MalformedFile("Could not convert field value into integer: " + fieldValue);
}
break;
case GencodeGTFFieldConstants.EXON_ID:
baseData.exonId = fieldValue;
break;
case GencodeGTFFieldConstants.LEVEL:
baseData.locusLevel = fieldValue;
break;
default:
optionalField = new OptionalField<>(fieldName, fieldValue);
break;
}
// If the optional field was good, we add it:
if ( optionalField != null ) {
baseData.optionalFields.add(optionalField);
}
}
}
/**
* Converts the given {@link String} into a {@link Strand}.
* @param s {@link String} to convert into a {@link Strand}.
* @return The {@link Strand} corresponding to {@code s}.
*/
private static Strand convertStringToStrand( final String s ) {
if ( s.equals("+") ) {
return Strand.POSITIVE;
}
else if ( s.equals("-") ) {
return Strand.NEGATIVE;
}
else {
throw new IllegalArgumentException("Unexpected value: " + s);
}
}
/**
* Populate this GencodeGtfFeature with the given data.
*/
protected GencodeGtfFeature(final GencodeGtfFeatureBaseData baseData) {
this.baseData = baseData;
}
// ================================================================================================
/**
* Create the appropriate {@link GencodeGtfFeature} object based on the given {@code baseData}
* @param baseData A {@link GencodeGtfFeatureBaseData} object containing all data for a single line in a GENCODE GTF File.
* @return A {@link GencodeGtfFeature} containing the data in {@code baseData}
*/
public static GencodeGtfFeature create(final GencodeGtfFeatureBaseData baseData) {
Utils.nonNull(baseData);
// Create our feature:
return baseData.featureType.create(baseData);
}
/**
* Create a {@link GencodeGtfFeature} based on a line from a Gencode GTF File.
* @param gtfLine A line from a Gencode GTF File to convert into a {@link GencodeGtfFeature} object.
* @param gtfFileType A {@link String} containing the file type of the GTF data that created this {@link GencodeGtfFeature}.
* @return The {@link GencodeGtfFeature} representing the information in {@code gtfLine}
*/
public static GencodeGtfFeature create(final String gtfLine, final String gtfFileType) {
Utils.nonNull(gtfLine);
return create(gtfLine.split(FIELD_DELIMITER), gtfFileType);
}
/**
* Create a {@link GencodeGtfFeature} based on a line from a Gencode GTF File.
* @param gtfFields A line from a Gencode GTF File split on the {@link #FIELD_DELIMITER} character.
* @param gtfFileType A {@link String} containing the file type of the GTF data that created this {@link GencodeGtfFeature}.
* @return The {@link GencodeGtfFeature} representing the information in {@code gtfLine}
*/
public static GencodeGtfFeature create(final String[] gtfFields, final String gtfFileType) {
Utils.nonNull(gtfFields);
// Ensure that the input data are superficially well-formed:
if ( gtfFields.length != GencodeGtfCodec.NUM_COLUMNS ) {
throw new UserException.MalformedFile("Invalid number of fields in the given GENCODE line " +
" - Given: " + gtfFields.length + " Expected: " + GencodeGtfCodec.NUM_COLUMNS);
}
final FeatureType featureType = FeatureType.getEnum( gtfFields[FEATURE_TYPE_INDEX] );
// Return our feature:
return featureType.create(gtfFields, gtfFileType);
}
// ================================================================================================
@Override
public String getContig() {
return baseData.genomicPosition.getContig();
}
@Override
public int getStart() {
return baseData.genomicPosition.getStart();
}
@Override
public int getEnd() {
return baseData.genomicPosition.getEnd();
}
// ================================================================================================
/**
* Get all the features from this {@link GencodeGtfFeature} itself.
* This is useful to get any subfeatures included in this {@link GencodeGtfFeature}.
* @return A {@link List} of the features represented in this {@link GencodeGtfFeature}.
*/
@VisibleForTesting
public List getAllFeatures() {
final List list = new ArrayList<>();
list.add(this);
return list;
}
/**
* Get all the {@link GencodeGtfFeatureBaseData} objects from this {@link GencodeGtfFeature} itself.
* This is useful to get any subfeatures included in this {@link GencodeGtfFeature}.
* @return A {@link List} of the {@link GencodeGtfFeatureBaseData} objects represented in this {@link GencodeGtfFeature}.
*/
@VisibleForTesting
List GencodeGtfFeatureBaseData() {
final List baseDataParts = new ArrayList<>();
baseDataParts.add(this.baseData);
getAllFeatures().forEach(feature -> baseDataParts.add(feature.baseData));
return baseDataParts;
}
/**
* Serializes the base data in {@link GencodeGtfFeature} to a string.
* @return a {@link String} representing this {@link GencodeGtfFeature}
*/
private String serializeToStringHelper() {
final StringBuilder stringBuilder = new StringBuilder();
stringBuilder.append( baseData.genomicPosition.getContig() );
stringBuilder.append( '\t' );
stringBuilder.append( baseData.annotationSource );
stringBuilder.append( '\t' );
stringBuilder.append( baseData.featureType );
stringBuilder.append( '\t' );
stringBuilder.append( baseData.genomicPosition.getStart() );
stringBuilder.append( '\t' );
stringBuilder.append( baseData.genomicPosition.getEnd() );
stringBuilder.append( "\t.\t" );
stringBuilder.append( baseData.genomicStrand );
stringBuilder.append( '\t' );
stringBuilder.append( baseData.genomicPhase );
stringBuilder.append( '\t' );
if ( baseData.geneId != null ) {
stringBuilder.append("gene_id \"");
stringBuilder.append(baseData.geneId);
stringBuilder.append( "\"; " );
}
if ( baseData.transcriptId != null) {
stringBuilder.append("transcript_id \"");
stringBuilder.append(baseData.transcriptId);
stringBuilder.append( "\"; " );
}
if ( baseData.geneType != null ) {
stringBuilder.append("gene_type \"");
stringBuilder.append(baseData.geneType);
stringBuilder.append( "\"; " );
}
if ( baseData.geneStatus != null ) {
stringBuilder.append("gene_status \"");
stringBuilder.append(baseData.geneStatus);
stringBuilder.append( "\"; " );
}
if ( baseData.geneName != null ) {
stringBuilder.append("gene_name \"");
stringBuilder.append(baseData.geneName);
stringBuilder.append( "\"; " );
}
if ( baseData.transcriptType != null ) {
stringBuilder.append("transcript_type \"");
stringBuilder.append(baseData.transcriptType);
stringBuilder.append( "\"; " );
}
if ( baseData.transcriptStatus != null ) {
stringBuilder.append("transcript_status \"");
stringBuilder.append(baseData.transcriptStatus);
stringBuilder.append( "\"; " );
}
if ( baseData.transcriptName != null ) {
stringBuilder.append("transcript_name \"");
stringBuilder.append(baseData.transcriptName);
stringBuilder.append( "\"; " );
}
if ( baseData.exonNumber != NO_EXON_NUMBER ) {
stringBuilder.append("exon_number ");
stringBuilder.append(baseData.exonNumber);
stringBuilder.append( "; " );
}
if ( baseData.exonId != null) {
stringBuilder.append("exon_id \"");
stringBuilder.append(baseData.exonId);
stringBuilder.append( "\"; ");
}
if (baseData.locusLevel != null) {
stringBuilder.append("level ");
stringBuilder.append(baseData.locusLevel);
stringBuilder.append("; ");
}
// = = = = = = = = = = = = = = = = = = = = = = =
// Output our optional fields:
stringBuilder.append(
baseData.optionalFields.stream().map(Object::toString).collect(Collectors.joining(" "))
);
return stringBuilder.toString().trim();
}
/**
* Serializes all data in {@link GencodeGtfFeature} to a string.
* This includes all subfields of child classes.
* @return a {@link String} representing this {@link GencodeGtfFeature}
*/
public String serializeToString() {
final StringBuilder stringBuilder = new StringBuilder();
final List features = getAllFeatures();
Collections.sort( features );
for ( final GencodeGtfFeature feature : features ) {
stringBuilder.append( feature.serializeToStringHelper() );
stringBuilder.append("\n");
}
return stringBuilder.toString().trim();
}
@Override
public String toString() {
return serializeToString();
}
// ================================================================================================
public String getGtfSourceFileType() { return baseData.gtfSourceFileType; }
public String getUcscGenomeVersion() {
return ucscGenomeVersion;
}
public void setUcscGenomeVersion(final String ucscGenomeVersion) {
this.ucscGenomeVersion = ucscGenomeVersion;
}
public SimpleInterval getGenomicPosition() { return baseData.genomicPosition; }
public int getFeatureOrderNumber() { return baseData.featureOrderNumber; }
public String getChromosomeName() {
return baseData.genomicPosition.getContig();
}
public String getAnnotationSource() {
return baseData.annotationSource;
}
public FeatureType getFeatureType() {
return baseData.featureType;
}
public int getGenomicStartLocation() {
return baseData.genomicPosition.getStart();
}
public int getGenomicEndLocation() {
return baseData.genomicPosition.getEnd();
}
public Strand getGenomicStrand() {
return baseData.genomicStrand;
}
public GenomicPhase getGenomicPhase() {
return baseData.genomicPhase;
}
public String getGeneId() {
return baseData.geneId;
}
public String getTranscriptId() {
return baseData.transcriptId;
}
public String getGeneType() {
return baseData.geneType;
}
public String getGeneName() {
return baseData.geneName;
}
public String getTranscriptType() {
return baseData.transcriptType;
}
public String getTranscriptName() {
return baseData.transcriptName;
}
public String getGeneStatus() {
return baseData.geneStatus;
}
public String getTranscriptStatus() {
return baseData.transcriptStatus;
}
public int getExonNumber() {
return baseData.exonNumber;
}
public String getExonId() {
return baseData.exonId;
}
public String getLocusLevel() {
return baseData.locusLevel;
}
public List> getOptionalFields() {
return baseData.optionalFields;
}
// Certian optional fields support multiple values (for example "tag"), so we need to return a list of them.
public List> getOptionalField(final String key) {
final List> optionalFields = new ArrayList<>();
for (final OptionalField optionalField : baseData.optionalFields) {
if ( optionalField.getName().equals(key) ) {
optionalFields.add(optionalField);
}
}
return optionalFields;
}
/**
* Comparable interface implementation for {@link GencodeGtfFeature}.
*
* Order is determined by {@link GencodeGtfFeatureBaseData#featureOrderNumber}
*
* @param other {@link GencodeGtfFeature} to which to compare
* @return -1 if this < other; 0 if this == other; 1 if this > other
*/
@Override
public int compareTo(final GencodeGtfFeature other) {
Utils.nonNull(other);
return (baseData.featureOrderNumber - other.baseData.featureOrderNumber);
}
@Override
public boolean equals(final Object that) {
if (that == null) {
return false;
}
else if ( this == that ) {
return true;
}
boolean isEqual = that instanceof GencodeGtfFeature;
if (isEqual) {
final GencodeGtfFeature thatFeature = (GencodeGtfFeature) that;
isEqual = Objects.equals(baseData, thatFeature.baseData);
if ( isEqual ) {
isEqual = ucscGenomeVersion.equals( thatFeature.getUcscGenomeVersion() );
}
}
return isEqual;
}
@Override
public int hashCode() {
return baseData != null ? baseData.hashCode() : 0;
}
/**
* Checks if {@code other} is contained within this {@link GencodeGtfFeature}.
* Comparison is made using {@link SimpleInterval#contains(Locatable)} ala {@link GencodeGtfFeatureBaseData#genomicPosition}
* @param other {@link Locatable} of which to check the bounds.
* @return true if {@code other} is contained within the bounds of this {@link GencodeGtfFeature}, false otherwise.
*/
public boolean contains(final Locatable other) {
return baseData.genomicPosition.contains(other);
}
/**
* Checks if {@code other} overlaps with this {@link GencodeGtfFeature}.
* Comparison is made using {@link SimpleInterval#overlaps(Locatable)} ala {@link GencodeGtfFeatureBaseData#genomicPosition}
* @param other {@link Locatable}-derived class of which to check the bounds.
* @return true if {@code other} overlaps the bounds of this {@link GencodeGtfFeature}, false otherwise.
*/
public boolean overlaps(final Locatable other) {
return baseData.genomicPosition.overlaps(other);
}
public void setFeatureOrderNumber(final int featureOrderNumber) {
this.baseData.featureOrderNumber = featureOrderNumber;
}
// ================================================================================================
static public class OptionalField {
private String name;
private T value;
public OptionalField(final String name, final T value) {
this.name = name;
this.value = value;
}
public String getName() {
return name;
}
public void setName(final String name) {
this.name = name;
}
public T getValue() {
return value;
}
public void setValue(final T value) {
this.value = value;
}
@Override
public String toString() {
final StringBuilder sb = new StringBuilder();
sb.append(name);
sb.append(" ");
// We need to do some formatting for the numbers / non-numbers in the field:
final String valueString = value.toString();
if ( NUMBER_PATTERN.matcher(valueString).matches() ) {
sb.append(valueString);
sb.append(";");
}
else {
sb.append("\"");
sb.append(valueString);
sb.append("\";");
}
return sb.toString();
}
@Override
public int hashCode() {
int result = name != null ? name.hashCode() : 0;
result = 31 * result + (value != null ? value.hashCode() : 0);
return result;
}
@Override
public boolean equals(final Object other) {
if (other == null) {
return false;
}
else if ( this == other ) {
return true;
}
if ( !(other instanceof OptionalField) ) {
return false;
}
final OptionalField otherOptionalField = (OptionalField) other;
return (name.equals(otherOptionalField.name)) &&
(value.equals(otherOptionalField.value));
}
}
// ================================================================================================
// ================================================================================================
/**
* Keyword identifying the source of the feature, like a program
* (e.g. Augustus or RepeatMasker) or an organization (like TAIR).
*
* For more information, see:
* https://www.gencodegenes.org/data_format.html
* https://en.wikipedia.org/wiki/General_feature_format
*/
public enum AnnotationSource {
ENSEMBL,
HAVANA,
ena // From ENSEMBLE GTFs
}
/**
* Type of the feature represented in a single line of a GENCODE GTF File.
*
* For more information, see:
* https://www.gencodegenes.org/data_format.html
* https://en.wikipedia.org/wiki/General_feature_format
*/
public enum FeatureType {
GENE("gene"){
public GencodeGtfFeature create(final GencodeGtfFeatureBaseData baseData) {
return GencodeGtfGeneFeature.create(baseData);
}
public GencodeGtfFeature create(final String[] gtfFields, final String gtfFileType) {
return GencodeGtfGeneFeature.create(gtfFields, gtfFileType);
}
},
TRANSCRIPT("transcript"){
public GencodeGtfFeature create(final GencodeGtfFeatureBaseData baseData) {
return GencodeGtfTranscriptFeature.create(baseData);
}
public GencodeGtfFeature create(final String[] gtfFields, final String gtfFileType) {
return GencodeGtfTranscriptFeature.create(gtfFields, gtfFileType);
}
},
SELENOCYSTEINE("Selenocysteine"){
public GencodeGtfFeature create(final GencodeGtfFeatureBaseData baseData) {
return GencodeGtfSelenocysteineFeature.create(baseData);
}
public GencodeGtfFeature create(final String[] gtfFields, final String gtfFileType) {
return GencodeGtfSelenocysteineFeature.create(gtfFields, gtfFileType);
}
},
EXON("exon"){
public GencodeGtfFeature create(final GencodeGtfFeatureBaseData baseData) {
return GencodeGtfExonFeature.create(baseData);
}
public GencodeGtfFeature create(final String[] gtfFields, final String gtfFileType) {
return GencodeGtfExonFeature.create(gtfFields, gtfFileType);
}
},
CDS("CDS"){
public GencodeGtfFeature create(final GencodeGtfFeatureBaseData baseData) {
return GencodeGtfCDSFeature.create(baseData);
}
public GencodeGtfFeature create(final String[] gtfFields, final String gtfFileType) {
return GencodeGtfCDSFeature.create(gtfFields, gtfFileType);
}
},
START_CODON("start_codon"){
public GencodeGtfFeature create(final GencodeGtfFeatureBaseData baseData) {
return GencodeGtfStartCodonFeature.create(baseData);
}
public GencodeGtfFeature create(final String[] gtfFields, final String gtfFileType) {
return GencodeGtfStartCodonFeature.create(gtfFields, gtfFileType);
}
},
STOP_CODON("stop_codon"){
public GencodeGtfFeature create(final GencodeGtfFeatureBaseData baseData) {
return GencodeGtfStopCodonFeature.create(baseData);
}
public GencodeGtfFeature create(final String[] gtfFields, final String gtfFileType) {
return GencodeGtfStopCodonFeature.create(gtfFields, gtfFileType);
}
},
UTR("UTR"){
public GencodeGtfFeature create(final GencodeGtfFeatureBaseData baseData) {
return GencodeGtfUTRFeature.create(baseData);
}
public GencodeGtfFeature create(final String[] gtfFields, final String gtfFileType) {
return GencodeGtfUTRFeature.create(gtfFields, gtfFileType);
}
};
@SuppressWarnings("unchecked")
private static final Map VALUE_MAP =
Arrays.stream(values()).collect(Collectors.toMap(v -> v.serialized.toLowerCase(), v -> v));
private final String serialized;
FeatureType(final String serializedValue) { serialized = serializedValue; }
@Override
public String toString() { return serialized; }
public static FeatureType getEnum(final String s) {
final String lowerS = s.toLowerCase();
if ( VALUE_MAP.containsKey(lowerS) ){
return VALUE_MAP.get(lowerS);
}
throw new IllegalArgumentException("Unexpected value: " + s);
}
/**
* Create a {@link GencodeGtfFeature} of this type given {@code baseData}
* @param baseData The data to use to create a {@link GencodeGtfFeature}
* @return The {@link GencodeGtfFeature} represented by the given {@code baseData}
*/
abstract public GencodeGtfFeature create(final GencodeGtfFeatureBaseData baseData);
/**
* Create a {@link GencodeGtfFeature} of this type given {@code gtfFields}
* @param gtfFields The data to use to create a {@link GencodeGtfFeature}
* @param gtfFileType A {@link String} containing the file type of the GTF data that created this {@link GencodeGtfFeature}.
* @return The {@link GencodeGtfFeature} represented by the given {@code gtfFields}
*/
abstract public GencodeGtfFeature create(final String[] gtfFields, final String gtfFileType);
}
/**
* Whether the first base of the CDS segment is the first (frame 0), second (frame 1) or third (frame 2) \
* in the codon of the ORF.
*
* For more information, see:
* https://www.gencodegenes.org/data_format.html
* https://en.wikipedia.org/wiki/General_feature_format
*/
public enum GenomicPhase {
ZERO("0"),
ONE ("1"),
TWO ("2"),
DOT (".");
@SuppressWarnings("unchecked")
private static final Map VALUE_MAP =
Arrays.stream(values()).collect(Collectors.toMap(v -> v.serialized.toLowerCase(), v -> v));
private final String serialized;
GenomicPhase(final String serializedValue) {
serialized = serializedValue;
}
@Override
public String toString() {
return serialized;
}
public static GenomicPhase getEnum(final String s) {
final String lowerS = s.toLowerCase();
if ( VALUE_MAP.containsKey(lowerS) ){
return VALUE_MAP.get(lowerS);
}
throw new IllegalArgumentException("Unexpected value: " + s);
}
}
}
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