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/*
dsh-bio-assembly Assemblies.
Copyright (c) 2013-2024 held jointly by the individual authors.
This library is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation; either version 3 of the License, or (at
your option) any later version.
This library is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; with out even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
License for more details.
You should have received a copy of the GNU Lesser General Public License
along with this library; if not, write to the Free Software Foundation,
Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
> http://www.fsf.org/licensing/licenses/lgpl.html
> http://www.opensource.org/licenses/lgpl-license.php
*/
package org.dishevelled.bio.assembly.gfa1;
import static com.google.common.base.Preconditions.checkArgument;
import static com.google.common.base.Preconditions.checkNotNull;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.Optional;
import javax.annotation.Nullable;
import javax.annotation.concurrent.Immutable;
import com.google.common.base.Joiner;
import com.google.common.base.Splitter;
import com.google.common.collect.ImmutableMap;
import org.dishevelled.bio.annotation.Annotation;
/**
* Link GFA 1.0 record.
*
* @author Michael Heuer
*/
@Immutable
public final class Link extends Gfa1Record {
/** Source reference for this link. */
private final Reference source;
/** Target reference for this link. */
private final Reference target;
/** Overlap for this link. */
private final String overlap;
/** Cached hash code. */
private final int hashCode;
/**
* Create a new link GFA 1.0 record.
*
* @param source source reference, must not be null
* @param target target reference, must not be null
* @param overlap overlap, if any
* @param annotations annotations, must not be null
*/
public Link(final Reference source,
final Reference target,
@Nullable final String overlap,
final Map annotations) {
super(annotations);
checkNotNull(source);
checkNotNull(target);
this.source = source;
this.target = target;
this.overlap = overlap;
hashCode = Objects.hash(this.source, this.target, this.overlap, getAnnotations());
}
/**
* Return the source reference for this link.
*
* @return the source reference for this link
*/
public Reference getSource() {
return source;
}
/**
* Return the target reference for this link.
*
* @return the target reference for this link
*/
public Reference getTarget() {
return target;
}
/**
* Return true if this link has an overlap in cigar format.
*
* @return true if this link has an overlap in cigar format.
*/
public boolean hasOverlap() {
return overlap != null;
}
/**
* Return the overlap in cigar format for this link, if any.
*
* @return the overlap in cigar format for this link, if any
*/
public String getOverlap() {
return overlap;
}
/**
* Return an optional wrapping the overlap in cigar format for this link.
*
* @return an optional wrapping the overlap in cigar format for this link
*/
public Optional getOverlapOpt() {
return Optional.ofNullable(overlap);
}
// optional fields
/**
* Return true if the annotations for this link contain
* the reserved key MQ.
*
* @return true if the annotations for this link contain
* the reserved key MQ
*/
public boolean containsMq() {
return containsAnnotationKey("MQ");
}
/**
* Return the Type=i value for the reserved key MQ
* as an integer.
*
* @return the Type=i value for the reserved key MQ
* as an integer
*/
public int getMq() {
return getAnnotationInteger("MQ");
}
/**
* Return an optional Type=i value for the reserved key MQ
* as an integer.
*
* @return an optional Type=i value for the reserved key MQ
* as an integer
*/
public Optional getMqOpt() {
return getAnnotationIntegerOpt("MQ");
}
/**
* Return true if the annotations for this link contain
* the reserved key MQ, for mapping quality.
*
* @return true if the annotations for this link contain
* the reserved key MQ, for mapping quality
*/
public boolean containsMappingQuality() {
return containsMq();
}
/**
* Return the mapping quality for this link (Type=i value for
* the reserved key MQ as an integer).
*
* @return the mapping quality for this link (Type=i value for
* the reserved key MQ as an integer)
*/
public int getMappingQuality() {
return getMq();
}
/**
* Return an optional wrapping the mapping quality for this link
* (Type=i value for the reserved key MQ as an integer).
*
* @return an optional wrapping the mapping quality for this link
* (Type=i value for the reserved key MQ as an integer)
*/
public Optional getMappingQualityOpt() {
return getMqOpt();
}
//
/**
* Return true if the annotations for this link contain
* the reserved key NM.
*
* @return true if the annotations for this link contain
* the reserved key NM
*/
public boolean containsNm() {
return containsAnnotationKey("NM");
}
/**
* Return the Type=i value for the reserved key NM
* as an integer.
*
* @return the Type=i value for the reserved key NM
* as an integer
*/
public int getNm() {
return getAnnotationInteger("NM");
}
/**
* Return an optional Type=i value for the reserved key NM
* as an integer.
*
* @return an optional Type=i value for the reserved key NM
* as an integer
*/
public Optional getNmOpt() {
return getAnnotationIntegerOpt("NM");
}
/**
* Return true if the annotations for this link contain
* the reserved key NM, for mismatch count.
*
* @return true if the annotations for this link contain
* the reserved key NM, for mismatch count
*/
public boolean containsMismatchCount() {
return containsNm();
}
/**
* Return the mismatch count for this link (Type=i value for
* the reserved key NM as an integer).
*
* @return the mismatch count for this link (Type=i value for
* the reserved key NM as an integer)
*/
public int getMismatchCount() {
return getNm();
}
/**
* Return an optional wrapping the mismatch count for this link
* (Type=i value for the reserved key NM as an integer).
*
* @return an optional wrapping the mismatch count for this link
* (Type=i value for the reserved key NM as an integer)
*/
public Optional getMismatchCountOpt() {
return getNmOpt();
}
//
/**
* Return true if the annotations for this link contain
* the reserved key RC.
*
* @return true if the annotations for this link contain
* the reserved key RC
*/
public boolean containsRc() {
return containsAnnotationKey("RC");
}
/**
* Return the Type=i value for the reserved key RC
* as an integer.
*
* @return the Type=i value for the reserved key RC
* as an integer
*/
public int getRc() {
return getAnnotationInteger("RC");
}
/**
* Return an optional Type=i value for the reserved key RC
* as an integer.
*
* @return an optional Type=i value for the reserved key RC
* as an integer
*/
public Optional getRcOpt() {
return getAnnotationIntegerOpt("RC");
}
/**
* Return true if the annotations for this link contain
* the reserved key RC, for read count.
*
* @return true if the annotations for this link contain
* the reserved key RC, for read count
*/
public boolean containsReadCount() {
return containsRc();
}
/**
* Return the read count for this link (Type=i value for
* the reserved key RC as an integer).
*
* @return the read count for this link (Type=i value for
* the reserved key RC as an integer)
*/
public int getReadCount() {
return getRc();
}
/**
* Return an optional wrapping the read count for this link
* (Type=i value for the reserved key RC as an integer).
*
* @return an optional wrapping the read count for this link
* (Type=i value for the reserved key RC as an integer)
*/
public Optional getReadCountOpt() {
return getRcOpt();
}
//
/**
* Return true if the annotations for this link contain
* the reserved key FC.
*
* @return true if the annotations for this link contain
* the reserved key FC
*/
public boolean containsFc() {
return containsAnnotationKey("FC");
}
/**
* Return the Type=i value for the reserved key FC
* as an integer.
*
* @return the Type=i value for the reserved key FC
* as an integer
*/
public int getFc() {
return getAnnotationInteger("FC");
}
/**
* Return an optional Type=i value for the reserved key FC
* as an integer.
*
* @return an optional Type=i value for the reserved key FC
* as an integer
*/
public Optional getFcOpt() {
return getAnnotationIntegerOpt("FC");
}
/**
* Return true if the annotations for this link contain
* the reserved key FC, for fragment count.
*
* @return true if the annotations for this link contain
* the reserved key FC, for fragment count
*/
public boolean containsFragmentCount() {
return containsFc();
}
/**
* Return the fragment count for this link (Type=i value for
* the reserved key FC as an integer).
*
* @return the fragment count for this link (Type=i value for
* the reserved key FC as an integer)
*/
public int getFragmentCount() {
return getFc();
}
/**
* Return an optional wrapping the fragment count for this link
* (Type=i value for the reserved key FC as an integer).
*
* @return an optional wrapping the fragment count for this link
* (Type=i value for the reserved key FC as an integer)
*/
public Optional getFragmentCountOpt() {
return getFcOpt();
}
//
/**
* Return true if the annotations for this link contain
* the reserved key KC.
*
* @return true if the annotations for this link contain
* the reserved key KC
*/
public boolean containsKc() {
return containsAnnotationKey("KC");
}
/**
* Return the Type=i value for the reserved key KC
* as an integer.
*
* @return the Type=i value for the reserved key KC
* as an integer
*/
public int getKc() {
return getAnnotationInteger("KC");
}
/**
* Return an optional Type=i value for the reserved key KC
* as an integer.
*
* @return an optional Type=i value for the reserved key KC
* as an integer
*/
public Optional getKcOpt() {
return getAnnotationIntegerOpt("KC");
}
/**
* Return true if the annotations for this link contain
* the reserved key KC, for k-mer count.
*
* @return true if the annotations for this link contain
* the reserved key KC, for k-mer count
*/
public boolean containsKmerCount() {
return containsKc();
}
/**
* Return the k-mer count for this link (Type=i value for
* the reserved key KC as an integer).
*
* @return the k-mer count for this link (Type=i value for
* the reserved key KC as an integer)
*/
public int getKmerCount() {
return getKc();
}
/**
* Return an optional wrapping the k-mer count for this link
* (Type=i value for the reserved key KC as an integer).
*
* @return an optional wrapping the k-mer count for this link
* (Type=i value for the reserved key KC as an integer)
*/
public Optional getKmerCountOpt() {
return getKcOpt();
}
//
/**
* Return true if the annotations for this link contain
* the reserved key ID.
*
* @return true if the annotations for this link contain
* the reserved key ID
*/
public boolean containsId() {
return containsAnnotationKey("ID");
}
/**
* Return the Type=Z value for the reserved key ID
* as a string.
*
* @return the Type=Z value for the reserved key ID
* as a string
*/
public String getId() {
return getAnnotationString("ID");
}
/**
* Return an optional Type=Z value for the reserved key ID
* as a string.
*
* @return an optional Type=Z value for the reserved key ID
* as a string
*/
public Optional getIdOpt() {
return getAnnotationStringOpt("ID");
}
@Override
public int hashCode() {
return hashCode;
}
@Override
public boolean equals(final Object o) {
if (o == this) {
return true;
}
if (!(o instanceof Link)) {
return false;
}
Link l = (Link) o;
return Objects.equals(source, l.getSource())
&& Objects.equals(target, l.getTarget())
&& Objects.equals(overlap, l.getOverlap())
&& Objects.equals(getAnnotations(), l.getAnnotations());
}
@Override
public String toString() {
Joiner joiner = Joiner.on("\t");
StringBuilder sb = new StringBuilder();
joiner.appendTo(sb, "L", source.splitToString(), target.splitToString(), overlap == null ? "*" : overlap);
if (!getAnnotations().isEmpty()) {
sb.append("\t");
joiner.appendTo(sb, getAnnotations().values());
}
return sb.toString();
}
/**
* Parse a link GFA 1.0 record from the specified value.
*
* @param value value, must not be null
* @return a link GFA 1.0 record parsed from the specified value
*/
public static Link valueOf(final String value) {
checkNotNull(value);
checkArgument(value.startsWith("L"), "link value must start with L");
List tokens = Splitter.on("\t").splitToList(value);
if (tokens.size() < 6) {
throw new IllegalArgumentException("link value must have at least six tokens, was " + tokens.size());
}
Reference source = Reference.splitValueOf(tokens.get(1), tokens.get(2));
Reference target = Reference.splitValueOf(tokens.get(3), tokens.get(4));
String overlap = "*".equals(tokens.get(5)) ? null : tokens.get(5);
ImmutableMap.Builder annotations = ImmutableMap.builder();
for (int i = 6; i < tokens.size(); i++) {
String token = tokens.get(i);
if (!token.isEmpty()) {
Annotation annotation = Annotation.valueOf(token);
annotations.put(annotation.getName(), annotation);
}
}
return new Link(source, target, overlap, annotations.build());
}
}
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