org.dishevelled.bio.assembly.gfa2.Fragment 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.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;
/**
* Fragment GFA 2.0 record.
*
* @author Michael Heuer
*/
@Immutable
public final class Fragment extends Gfa2Record {
/** Segment identifier for this fragment. */
private final String segmentId;
/** External reference for this fragment. */
private final Reference external;
/** Segment start position for this fragment. */
private final Position segmentStart;
/** Segment end position for this fragment. */
private final Position segmentEnd;
/** Fragment start position for this fragment. */
private final Position fragmentStart;
/** Fragment end position for this fragment. */
private final Position fragmentEnd;
/** Optional alignment for this fragment. */
private final Alignment alignment;
/** Cached hash code. */
private final int hashCode;
/**
* Create a new fragment GFA 2.0 record.
*
* @param segmentId segment identifier, must not be null
* @param external external reference, must not be null
* @param segmentStart segment start position, must not be null
* @param segmentEnd segment end position, must not be null
* @param fragmentStart fragment start position, must not be null
* @param fragmentEnd fragment end position, must not be null
* @param alignment alignment, if any
* @param annotations annotations, must not be null
*/
public Fragment(final String segmentId,
final Reference external,
final Position segmentStart,
final Position segmentEnd,
final Position fragmentStart,
final Position fragmentEnd,
@Nullable final Alignment alignment,
final Map annotations) {
super(annotations);
checkNotNull(segmentId);
checkNotNull(external);
checkNotNull(segmentStart);
checkNotNull(segmentEnd);
checkNotNull(fragmentStart);
checkNotNull(fragmentEnd);
this.segmentId = segmentId;
this.external = external;
this.segmentStart = segmentStart;
this.segmentEnd = segmentEnd;
this.fragmentStart = fragmentStart;
this.fragmentEnd = fragmentEnd;
this.alignment = alignment;
hashCode = Objects.hash(this.segmentId, this.external, this.segmentStart,
this.segmentEnd, this.fragmentStart, this.fragmentEnd,
this.alignment, getAnnotations());
}
/**
* Return the segment identifier for this fragment.
*
* @return the segment identifier for this fragment
*/
public String getSegmentId() {
return segmentId;
}
/**
* Return the external reference for this fragment.
*
* @return the external reference for this fragment
*/
public Reference getExternal() {
return external;
}
/**
* Return the segment start position for this fragment.
*
* @return the segment start position for this fragment
*/
public Position getSegmentStart() {
return segmentStart;
}
/**
* Return the segment end position for this fragment.
*
* @return the segment end position for this fragment
*/
public Position getSegmentEnd() {
return segmentEnd;
}
/**
* Return the fragment start position for this fragment.
*
* @return the fragment start position for this fragment
*/
public Position getFragmentStart() {
return fragmentStart;
}
/**
* Return the fragment end position for this fragment.
*
* @return the fragment end position for this fragment
*/
public Position getFragmentEnd() {
return fragmentEnd;
}
/**
* Return true if this fragment has an alignment.
*
* @since 1.3.2
* @return true if this fragment has an alignment
*/
public boolean hasAlignment() {
return alignment != null;
}
/**
* Return the alignment for this fragment, if any.
*
* @return the alignment for this fragment, if any
*/
public Alignment getAlignment() {
return alignment;
}
/**
* Return an optional wrapping the alignment for this fragment.
*
* @return an optional wrapping the alignment for this fragment
*/
public Optional getAlignmentOpt() {
return Optional.ofNullable(alignment);
}
// optional fields
/**
* Return true if the annotations for this fragment contain
* the reserved key TS.
*
* @since 1.3.2
* @return true if the annotations for this fragment 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 fragment contain
* the reserved key TS, for trace spacing.
*
* @since 1.3.2
* @return true if the annotations for this fragment contain
* the reserved key TS, for trace spacing
*/
public boolean containsTraceSpacing() {
return containsTs();
}
/**
* Return the trace spacing for this fragment (Type=i value for
* the reserved key TS as an integer).
*
* @since 1.3.2
* @return the trace spacing for this fragment (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 fragment
* (Type=i value for the reserved key TS as an integer).
*
* @since 1.3.2
* @return an optional wrapping the trace spacing for this fragment
* (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 Fragment)) {
return false;
}
Fragment f = (Fragment) o;
return Objects.equals(segmentId, f.getSegmentId())
&& Objects.equals(external, f.getExternal())
&& Objects.equals(segmentStart, f.getSegmentStart())
&& Objects.equals(segmentEnd, f.getSegmentEnd())
&& Objects.equals(fragmentStart, f.getFragmentStart())
&& Objects.equals(fragmentEnd, f.getFragmentEnd())
&& Objects.equals(alignment, f.getAlignment())
&& Objects.equals(getAnnotations(), f.getAnnotations());
}
@Override
public String toString() {
Joiner joiner = Joiner.on("\t");
StringBuilder sb = new StringBuilder();
joiner.appendTo(sb, "F", segmentId, external, segmentStart, segmentEnd, fragmentStart, fragmentEnd, alignment == null ? "*" : alignment);
if (!getAnnotations().isEmpty()) {
sb.append("\t");
joiner.appendTo(sb, getAnnotations().values());
}
return sb.toString();
}
/**
* Parse a fragment GFA 2.0 record from the specified value.
*
* @param value value, must not be null
* @return a fragment GFA 2.0 record parsed from the specified value
*/
public static Fragment valueOf(final String value) {
checkNotNull(value);
checkArgument(value.startsWith("F"), "fragment value must start with F");
List tokens = Splitter.on("\t").splitToList(value);
if (tokens.size() < 8) {
throw new IllegalArgumentException("fragment value must have at least eight tokens, was " + tokens.size());
}
String segmentId = tokens.get(1);
Reference external = Reference.valueOf(tokens.get(2));
Position segmentStart = Position.valueOf(tokens.get(3));
Position segmentEnd = Position.valueOf(tokens.get(4));
Position fragmentStart = Position.valueOf(tokens.get(5));
Position fragmentEnd = Position.valueOf(tokens.get(6));
Alignment alignment = Alignment.valueOf(tokens.get(7));
ImmutableMap.Builder annotations = ImmutableMap.builder();
for (int i = 8; i < tokens.size(); i++) {
String token = tokens.get(i);
if (!token.isEmpty()) {
Annotation annotation = Annotation.valueOf(token);
annotations.put(annotation.getName(), annotation);
}
}
return new Fragment(segmentId, external, segmentStart, segmentEnd, fragmentStart, fragmentEnd, alignment, annotations.build());
}
}
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