org.dishevelled.bio.assembly.gfa1.Containment Maven / Gradle / Ivy
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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;
/**
* Containment GFA 1.0 record.
*
* @author Michael Heuer
*/
@Immutable
public final class Containment extends Gfa1Record {
/** Container reference for this containment. */
private final Reference container;
/** Contained reference for this containment. */
private final Reference contained;
/** Position for this containment. */
private final int position;
/** Overlap in cigar format for this containment. */
private final String overlap;
/** Cached hash code. */
private final int hashCode;
/**
* Create a new containment GFA 1.0 record.
*
* @param container container reference, must not be null
* @param contained contained reference, must not be null
* @param position position, must be at least zero
* @param overlap overlap in cigar format, if any
* @param annotations annotations, must not be null
*/
public Containment(final Reference container,
final Reference contained,
final int position,
@Nullable final String overlap,
final Map annotations) {
super(annotations);
checkNotNull(container);
checkNotNull(contained);
checkArgument(position >= 0, "position must be at least zero, was " + position);
this.container = container;
this.contained = contained;
this.position = position;
this.overlap = overlap;
hashCode = Objects.hash(this.container, this.contained, this.position, this.overlap, getAnnotations());
}
/**
* Return the container reference for this containment.
*
* @return the container reference for this containment
*/
public Reference getContainer() {
return container;
}
/**
* Return the contained reference for this containment.
*
* @return the contained reference for this containment
*/
public Reference getContained() {
return contained;
}
/**
* Return the position for this containment (0-based coordinate system). The position is
* the leftmost position of the contained segment in the container segment in its forward
* orientation (i.e. before this is oriented according to the container reference orientation).
*
* @return the position for this containment (0-based coordinate system)
*/
public int getPosition() {
return position;
}
/**
* Return true if this containment has an overlap in cigar format.
*
* @return true if this containment has an overlap in cigar format.
*/
public boolean hasOverlap() {
return overlap != null;
}
/**
* Return the overlap in cigar format for this containment, if any.
*
* @return the overlap in cigar format for this containment, if any
*/
public String getOverlap() {
return overlap;
}
/**
* Return an optional wrapping the overlap in cigar format for this containment.
*
* @return an optional wrapping the overlap in cigar format for this containment
*/
public Optional getOverlapOpt() {
return Optional.ofNullable(overlap);
}
// optional fields
/**
* Return true if the annotations for this containment contain
* the reserved key RC.
*
* @return true if the annotations for this containment 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 containment contain
* the reserved key RC, for read count.
*
* @return true if the annotations for this containment contain
* the reserved key RC, for read count
*/
public boolean containsReadCount() {
return containsRc();
}
/**
* Return the read count for this containment (Type=i value for the
* reserved key RC as an integer).
*
* @return the read count for this containment (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 containment
* (Type=i value for the reserved key RC as an integer).
*
* @return an optional wrapping the read count for this containment
* (Type=i value for the reserved key RC as an integer)
*/
public Optional getReadCountOpt() {
return getRcOpt();
}
//
/**
* Return true if the annotations for this containment contain
* the reserved key NM.
*
* @return true if the annotations for this containment 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 containment contain
* the reserved key NM, for mismatch count.
*
* @return true if the annotations for this containment contain
* the reserved key NM, for mismatch count
*/
public boolean containsMismatchCount() {
return containsNm();
}
/**
* Return the mismatch count for this containment (Type=i value
* for the reserved key NM as an integer).
*
* @return the mismatch count for this containment (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 containment
* (Type=i value for the reserved key NM as an integer).
*
* @return an optional wrapping the mismatch count for this containment
* (Type=i value for the reserved key NM as an integer)
*/
public Optional getMismatchCountOpt() {
return getNmOpt();
}
//
/**
* Return true if the annotations for this containment contain
* the reserved key ID.
*
* @return true if the annotations for this containment 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 Containment)) {
return false;
}
Containment c = (Containment) o;
return Objects.equals(container, c.getContainer())
&& Objects.equals(contained, c.getContained())
&& Objects.equals(position, c.getPosition())
&& Objects.equals(overlap, c.getOverlap())
&& Objects.equals(getAnnotations(), c.getAnnotations());
}
@Override
public String toString() {
Joiner joiner = Joiner.on("\t");
StringBuilder sb = new StringBuilder();
joiner.appendTo(sb, "C", container.splitToString(), contained.splitToString(), position, overlap == null ? "*" : overlap);
if (!getAnnotations().isEmpty()) {
sb.append("\t");
joiner.appendTo(sb, getAnnotations().values());
}
return sb.toString();
}
/**
* Parse a containment GFA 1.0 record from the specified value.
*
* @param value value, must not be null
* @return a containment GFA 1.0 record parsed from the specified value
*/
public static Containment valueOf(final String value) {
checkNotNull(value);
checkArgument(value.startsWith("C"), "containment value must start with C");
List tokens = Splitter.on("\t").splitToList(value);
if (tokens.size() < 7) {
throw new IllegalArgumentException("containment value must have at least seven tokens, was " + tokens.size());
}
Reference container = Reference.splitValueOf(tokens.get(1), tokens.get(2));
Reference contained = Reference.splitValueOf(tokens.get(3), tokens.get(4));
int position = Integer.parseInt(tokens.get(5));
String overlap = "*".equals(tokens.get(6)) ? null : tokens.get(6);
ImmutableMap.Builder annotations = ImmutableMap.builder();
for (int i = 7; i < tokens.size(); i++) {
String token = tokens.get(i);
if (!token.isEmpty()) {
Annotation annotation = Annotation.valueOf(token);
annotations.put(annotation.getName(), annotation);
}
}
return new Containment(container, contained, position, overlap, annotations.build());
}
}
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