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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.gfa2;
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;
/**
* Gap GFA 2.0 record.
*
* @author Michael Heuer
*/
@Immutable
public final class Gap extends Gfa2Record {
/** Optional identifier for this gap. */
private final String id;
/** Source reference for this gap. */
private final Reference source;
/** Target reference for this gap. */
private final Reference target;
/** Distance for this gap. */
private final int distance;
/** Optional variance for this gap. */
private final Integer variance;
/** Cached hash code. */
private final int hashCode;
/**
* Create a new gap GFA 2.0 record.
*
* @param id identifier, if any
* @param source source reference, must not be null
* @param target target reference, must not be null
* @param distance distance, must be at least zero
* @param variance variance, if any
* @param annotations annotations, must not be null
*/
public Gap(@Nullable final String id,
final Reference source,
final Reference target,
final int distance,
@Nullable final Integer variance,
final Map annotations) {
super(annotations);
checkNotNull(source);
checkNotNull(target);
checkArgument(distance >= 0, "distance must be at least zero");
this.id = id;
this.source = source;
this.target = target;
this.distance = distance;
this.variance = variance;
hashCode = Objects.hash(this.id, this.source, this.target, this.distance,
this.variance, getAnnotations());
}
/**
* Return true if this gap has an identifier.
*
* @return true if this gap has an identifier
*/
public boolean hasId() {
return id != null;
}
/**
* Return the identifier for this gap, if any.
*
* @return the identifier for this gap, if any
*/
public String getId() {
return id;
}
/**
* Return an optional wrapping the identifier for this gap.
*
* @return an optional wrapping the identifier for this gap
*/
public Optional getIdOpt() {
return Optional.ofNullable(id);
}
/**
* Return the source reference for this gap.
*
* @return the source reference for this gap
*/
public Reference getSource() {
return source;
}
/**
* Return the target reference for this gap.
*
* @return the target reference for this gap
*/
public Reference getTarget() {
return target;
}
/**
* Return the distance for this gap.
*
* @return the distance for this gap
*/
public int getDistance() {
return distance;
}
/**
* Return true if this gap has a variance.
*
* @return true if this gap has a variance
*/
public boolean hasVariance() {
return variance != null;
}
/**
* Return the variance for this gap, if any.
*
* @return the variance for this gap, if any
*/
public Integer getVariance() {
return variance;
}
/**
* Return an optional wrapping the variance for this gap.
*
* @return an optional wrapping the variance for this gap
*/
public Optional getVarianceOpt() {
return Optional.ofNullable(variance);
}
// optional fields
/**
* Return true if the annotations for this gap contain
* the reserved key TS.
*
* @since 1.3.2
* @return true if the annotations for this gap contain
* the reserved key TS
*/
public boolean containsTs() {
return containsAnnotationKey("TS");
}
/**
* Return the Type=i value for the reserved key TS
* as an integer.
*
* @since 1.3.2
* @return the Type=i value for the reserved key TS
* as an integer
*/
public int getTs() {
return getAnnotationInteger("TS");
}
/**
* Return an optional Type=i value for the reserved key TS
* as an integer.
*
* @since 1.3.2
* @return an optional Type=i value for the reserved key TS
* as an integer
*/
public Optional getTsOpt() {
return getAnnotationIntegerOpt("TS");
}
/**
* Return true if the annotations for this gap contain
* the reserved key TS, for trace spacing.
*
* @since 1.3.2
* @return true if the annotations for this gap contain
* the reserved key TS, for trace spacing
*/
public boolean containsTraceSpacing() {
return containsTs();
}
/**
* Return the trace spacing for this gap (Type=i value for
* the reserved key TS as an integer).
*
* @since 1.3.2
* @return the trace spacing for this gap (Type=i value for
* the reserved key TS as an integer)
*/
public int getTraceSpacing() {
return getTs();
}
/**
* Return an optional wrapping the trace spacing for this gap
* (Type=i value for the reserved key TS as an integer).
*
* @since 1.3.2
* @return an optional wrapping the trace spacing for this gap
* (Type=i value for the reserved key TS as an integer)
*/
public Optional getTraceSpacingOpt() {
return getTsOpt();
}
@Override
public int hashCode() {
return hashCode;
}
@Override
public boolean equals(final Object o) {
if (o == this) {
return true;
}
if (!(o instanceof Gap)) {
return false;
}
Gap g = (Gap) o;
return Objects.equals(id, g.getId())
&& Objects.equals(source, g.getSource())
&& Objects.equals(target, g.getTarget())
&& Objects.equals(distance, g.getDistance())
&& Objects.equals(variance, g.getVariance())
&& Objects.equals(getAnnotations(), g.getAnnotations());
}
@Override
public String toString() {
Joiner joiner = Joiner.on("\t");
StringBuilder sb = new StringBuilder();
joiner.appendTo(sb, "G", id == null ? "*" : id, source, target, distance, variance == null ? "*" : variance);
if (!getAnnotations().isEmpty()) {
sb.append("\t");
joiner.appendTo(sb, getAnnotations().values());
}
return sb.toString();
}
/**
* Parse a gap GFA 2.0 record from the specified value.
*
* @param value value, must not be null
* @return a gap GFA 2.0 record parsed from the specified value
*/
public static Gap valueOf(final String value) {
checkNotNull(value);
checkArgument(value.startsWith("G"), "gap value must start with G");
List tokens = Splitter.on("\t").splitToList(value);
if (tokens.size() < 6) {
throw new IllegalArgumentException("gap value must have at least six tokens, was " + tokens.size());
}
String id = "*".equals(tokens.get(1)) ? null : tokens.get(1);
Reference source = Reference.valueOf(tokens.get(2));
Reference target = Reference.valueOf(tokens.get(3));
int distance = Integer.parseInt(tokens.get(4));
Integer variance = "*".equals(tokens.get(5)) ? null : Integer.parseInt(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 Gap(id, source, target, distance, variance, annotations.build());
}
}
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