org.dishevelled.bio.assembly.gfa1.Segment 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;
/**
* Segment GFA 1.0 record.
*
* @author Michael Heuer
*/
@Immutable
public final class Segment extends Gfa1Record {
/** Identifier for this segment. */
private final String id;
/** Optional sequence for this segment. */
private final String sequence;
/** Cached hash code. */
private final int hashCode;
/**
* Create a new segment GFA 1.0 record.
*
* @param id identifier, must not be null
* @param sequence sequence, if any
* @param annotations annotations, must not be null
*/
public Segment(final String id,
@Nullable final String sequence,
final Map annotations) {
super(annotations);
checkNotNull(id);
this.id = id;
this.sequence = sequence;
hashCode = Objects.hash(this.id, this.sequence, getAnnotations());
}
/**
* Return the identifier for this segment.
*
* @deprecated replaced by name field, to be removed in version 3.0
* @return the identifier for this segment
*/
public String getId() {
return id;
}
/**
* Return the name of this segment.
*
* @since 2.0.3
* @return the name of this segment
*/
public String getName() {
return getId();
}
/**
* Return true if this segment has a sequence.
*
* @return true if this segment has a sequence
*/
public boolean hasSequence() {
return sequence != null;
}
/**
* Return the sequence for this segment, if any.
*
* @return the sequence for this segment, if any
*/
public String getSequence() {
return sequence;
}
/**
* Return an optional wrapping the sequence for this segment.
*
* @return an optional wrapping the sequence for this segment
*/
public Optional getSequenceOpt() {
return Optional.ofNullable(sequence);
}
// optional fields
/**
* Return true if the annotations for this segment contain
* the reserved key LN.
*
* @return true if the annotations for this segment contain
* the reserved key LN
*/
public boolean containsLn() {
return containsAnnotationKey("LN");
}
/**
* Return the Type=i value for the reserved key LN
* as an integer.
*
* @return the Type=i value for the reserved key LN
* as an integer
*/
public int getLn() {
return getAnnotationInteger("LN");
}
/**
* Return an optional Type=i value for the reserved key LN
* as an integer.
*
* @return an optional Type=i value for the reserved key LN
* as an integer
*/
public Optional getLnOpt() {
return getAnnotationIntegerOpt("LN");
}
/**
* Return true if the annotations for this segment contain
* the reserved key LN, for length.
*
* @return true if the annotations for this segment contain
* the reserved key LN, for length
*/
public boolean containsLength() {
return containsLn();
}
/**
* Return the length of this segment (Type=i value for
* the reserved key LN as an integer).
*
* @return the length of this segment (Type=i value for
* the reserved key LN as an integer)
*/
public int getLength() {
return getLn();
}
/**
* Return an optional wrapping the length of this segment
* (Type=i value for the reserved key LN as an integer).
*
* @return an optional wrapping the length of this segment
* (Type=i value for the reserved key LN as an integer)
*/
public Optional getLengthOpt() {
return getLnOpt();
}
//
/**
* Return true if the annotations for this segment contain
* the reserved key RC.
*
* @return true if the annotations for this segment 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 segment contain
* the reserved key RC, for read count.
*
* @return true if the annotations for this segment contain
* the reserved key RC, for read count
*/
public boolean containsReadCount() {
return containsRc();
}
/**
* Return the read count for this segment (Type=i value for
* the reserved key RC as an integer).
*
* @return the read count for this segment (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 segment
* (Type=i value for the reserved key RC as an integer).
*
* @return an optional wrapping the read count for this segment
* (Type=i value for the reserved key RC as an integer)
*/
public Optional getReadCountOpt() {
return getRcOpt();
}
//
/**
* Return true if the annotations for this segment contain
* the reserved key FC.
*
* @return true if the annotations for this segment 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 segment contain
* the reserved key FC, for fragment count.
*
* @return true if the annotations for this segment contain
* the reserved key FC, for fragment count
*/
public boolean containsFragmentCount() {
return containsFc();
}
/**
* Return true if the annotations for this segment contain
* the reserved key FC, for fragment count.
*
* @return if the annotations for this segment contain
* the reserved key FC, for fragment count
*/
public int getFragmentCount() {
return getFc();
}
/**
* Return an optional wrapping the fragment count for this segment
* (Type=i value for the reserved key FC as an integer).
*
* @return an optional wrapping the fragment count for this segment
* (Type=i value for the reserved key FC as an integer)
*/
public Optional getFragmentCountOpt() {
return getFcOpt();
}
//
/**
* Return true if the annotations for this segment contain
* the reserved key KC.
*
* @return true if the annotations for this segment 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 segment contain
* the reserved key KC, for k-mer count.
*
* @return true if the annotations for this segment contain
* the reserved key KC, for k-mer count
*/
public boolean containsKmerCount() {
return containsKc();
}
/**
* Return the k-mer count for this segment (Type=i value for
* the reserved key KC as an integer).
*
* @return the k-mer count for this segment (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 segment
* (Type=i value for the reserved key KC as an integer).
*
* @return an optional wrapping the k-mer count for this segment
* (Type=i value for the reserved key KC as an integer)
*/
public Optional getKmerCountOpt() {
return getKcOpt();
}
//
/**
* Return true if the annotations for this segment contain
* the reserved key SH.
*
* @return true if the annotations for this segment contain
* the reserved key SH
*/
public boolean containsSh() {
return containsAnnotationKey("SH");
}
/**
* Return the Type=H value for the reserved key SH
* as a byte array.
*
* @return the Type=Z value for the reserved key SH
* as a byte array
*/
public byte[] getSh() {
return getAnnotationByteArray("SH");
}
/**
* Return an optional Type=H value for the reserved key SH
* as a byte array.
*
* @return an optional Type=H value for the reserved key SH
* as a byte array
*/
public Optional getShOpt() {
return getAnnotationByteArrayOpt("SH");
}
/**
* Return true if the annotations for this segment contain
* the reserved key SH, for SHA-256 checksum of the
* sequence.
*
* @return true if the annotations for this segment contain
* the reserved key SH, for SHA-256 checksum of the
* sequence
*/
public boolean containsSequenceChecksum() {
return containsSh();
}
/**
* Return the SHA-256 checksum of the sequence for this segment
* (Type=H value for the reserved key SH as a byte array).
*
* @return the SHA-256 checksum of the sequence for this segment
* (Type=H value for the reserved key SH as a byte array)
*/
public byte[] getSequenceChecksum() {
return getSh();
}
/**
* Return an optional wrapping the SHA-256 checksum of the sequence
* for this segment (Type=H value for the reserved key SH
* as a byte array).
*
* @return an optional wrapping the SHA-256 checksum of the sequence
* for this segment (Type=H value for the reserved key SH
* as a byte array)
*/
public Optional getSequenceChecksumOpt() {
return getShOpt();
}
//
/**
* Return true if the annotations for this segment contain
* the reserved key UR.
*
* @return true if the annotations for this segment contain
* the reserved key UR
*/
public boolean containsUr() {
return containsAnnotationKey("UR");
}
/**
* Return the Type=Z value for the reserved key UR
* as a string.
*
* @return the Type=Z value for the reserved key UR
* as a string
*/
public String getUr() {
return getAnnotationString("UR");
}
/**
* Return an optional Type=Z value for the reserved key UR
* as a string.
*
* @return an optional Type=Z value for the reserved key UR
* as a string
*/
public Optional getUrOpt() {
return getAnnotationStringOpt("UR");
}
/**
* Return true if the annotations for this segment contain
* the reserved key UR.
*
* @return true if the annotations for this segment contain
* the reserved key UR
*/
public boolean containsSequenceUri() {
return containsUr();
}
/**
* Return the URI or local file-system path of the sequence for
* this segment (Type=Z value for the reserved key UR
* as a string). If it does not start with a standard protocol
* (e.g. ftp), it is assumed to be a local path.
*
* @return the URI or local file-system path of the sequence for
* this segment (Type=Z value for the reserved key UR
* as a string)
*/
public String getSequenceUri() {
return getUr();
}
/**
* Return an optional wrapping the URI or local file-system path of
* the sequence for this segment (Type=Z value for the reserved key
* UR as a string). If it does not start with a standard
* protocol (e.g. ftp), it is assumed to be a local path.
*
* @return an optional wrapping the URI or local file-system path of
* the sequence for this segment (Type=Z value for the reserved key
* UR as a string)
*/
public Optional getSequenceUriOpt() {
return getUrOpt();
}
//
/**
* Return true if the annotations for this segment contain
* the rGFA reserved key SN.
*
* @return true if the annotations for this segment contain
* the rGFA reserved key SN
*/
public boolean containsSn() {
return containsAnnotationKey("SN");
}
/**
* Return the Type=Z value for the rGFA reserved key SN
* as a string.
*
* @return the Type=Z value for the rGFA reserved key SN
* as a string
*/
public String getSn() {
return getAnnotationString("SN");
}
/**
* Return an optional Type=Z value for the rGFA reserved key SN
* as a string.
*
* @return an optional Type=Z value for the rGFA reserved key SN
* as a string
*/
public Optional getSnOpt() {
return getAnnotationStringOpt("SN");
}
/**
* Return true if the annotations for this segment contain
* the rGFA reserved key SN.
*
* @return true if the annotations for this segment contain
* the rGFA reserved key SN
*/
public boolean containsStableName() {
return containsSn();
}
/**
* Return the name of stable sequence from which this segment is derived
* (Type=Z value for the rGFA reserved key SN as a string).
*
* @return the name of stable sequence from which this segment is derived
* (Type=Z value for the rGFA reserved key SN as a string)
*/
public String getStableName() {
return getSn();
}
/**
* Return an optional wrapping the name of stable sequence from which this
* segment is derived (Type=Z value for the rGFA reserved key SN
* as a string).
*
* @return an optional wrapping the name of stable sequence from which this
* segment is derived (Type=Z value for the rGFA reserved key SN
* as a string)
*/
public Optional getStableNameOpt() {
return getSnOpt();
}
//
/**
* Return true if the annotations for this segment contain
* the rGFA reserved key SO.
*
* @return true if the annotations for this segment contain
* the rGFA reserved key SO
*/
public boolean containsSo() {
return containsAnnotationKey("SO");
}
/**
* Return the Type=i value for the rGFA reserved key SO
* as an integer.
*
* @return the Type=i value for the rGFA reserved key SO
* as an integer
*/
public int getSo() {
return getAnnotationInteger("SO");
}
/**
* Return an optional Type=i value for the rGFA reserved key SO
* as an integer.
*
* @return an optional Type=i value for the rGFA reserved key SO
* as an integer
*/
public Optional getSoOpt() {
return getAnnotationIntegerOpt("SO");
}
/**
* Return true if the annotations for this segment contain
* the rGFA reserved key SO.
*
* @return true if the annotations for this segment contain
* the rGFA reserved key SO
*/
public boolean containsStableOffset() {
return containsSo();
}
/**
* Return the offset on the stable sequence for this segment
* (Type=i value for the rGFA reserved key SO as an integer).
*
* @return the offset on the stable sequence for this segment
* (Type=i value for the rGFA reserved key SO as an integer)
*/
public int getStableOffset() {
return getSo();
}
/**
* Return an optional wrapping the offset on the stable sequence for this
* segment (Type=i value for the rGFA reserved key SO
* as an integer).
*
* @return an optional wrapping the offset on the stable sequence for this
* segment (Type=i value for the rGFA reserved key SO
* as an integer)
*/
public Optional getStableOffsetOpt() {
return getSoOpt();
}
//
/**
* Return true if the annotations for this segment contain
* the rGFA reserved key SR.
*
* @return true if the annotations for this segment contain
* the rGFA reserved key SR
*/
public boolean containsSr() {
return containsAnnotationKey("SR");
}
/**
* Return the Type=i value for the rGFA reserved key SR
* as an integer.
*
* @return the Type=i value for the rGFA reserved key SR
* as an integer
*/
public int getSr() {
return getAnnotationInteger("SR");
}
/**
* Return an optional Type=i value for the rGFA reserved key SR
* as an integer.
*
* @return an optional Type=i value for the rGFA reserved key SR
* as an integer
*/
public Optional getSrOpt() {
return getAnnotationIntegerOpt("SR");
}
/**
* Return true if the annotations for this segment contain
* the rGFA reserved key SR.
*
* @return true if the annotations for this segment contain
* the rGFA reserved key SR
*/
public boolean containsStableRank() {
return containsSr();
}
/**
* Return the rank of the stable sequence for this segment
* (Type=i value for the rGFA reserved key SR as an integer).
*
* Rank is 0 if on a linear reference genome; >0 otherwise.
*
* @return the rank of the stable sequence for this segment
* (Type=i value for the rGFA reserved key SR as an integer)
*/
public int getStableRank() {
return getSr();
}
/**
* Return an optional wrapping the rank of the stable sequence for this
* segment (Type=i value for the rGFA reserved key SR
* as an integer).
*
* Rank is 0 if on a linear reference genome; >0 otherwise.
*
* @return an optional wrapping the rank of the stable sequence for this
* segment (Type=i value for the rGFA reserved key SR
* as an integer)
*/
public Optional getStableRankOpt() {
return getSrOpt();
}
@Override
public int hashCode() {
return hashCode;
}
@Override
public boolean equals(final Object o) {
if (o == this) {
return true;
}
if (!(o instanceof Segment)) {
return false;
}
Segment s = (Segment) o;
return Objects.equals(id, s.getId())
&& Objects.equals(sequence, s.getSequence())
&& Objects.equals(getAnnotations(), s.getAnnotations());
}
@Override
public String toString() {
Joiner joiner = Joiner.on("\t");
StringBuilder sb = new StringBuilder();
joiner.appendTo(sb, "S", id, sequence == null ? "*" : sequence);
if (!getAnnotations().isEmpty()) {
sb.append("\t");
joiner.appendTo(sb, getAnnotations().values());
}
return sb.toString();
}
/**
* Parse a segment GFA 1.0 record from the specified value.
*
* @param value value, must not be null
* @return a segment GFA 1.0 record parsed from the specified value
*/
public static Segment valueOf(final String value) {
checkNotNull(value);
checkArgument(value.startsWith("S"), "segment value must start with S");
List tokens = Splitter.on("\t").splitToList(value);
if (tokens.size() < 3) {
throw new IllegalArgumentException("segment value must have at least three tokens, was " + tokens.size());
}
String id = tokens.get(1);
String sequence = "*".equals(tokens.get(2)) ? null : tokens.get(2);
ImmutableMap.Builder annotations = ImmutableMap.builder();
for (int i = 3; i < tokens.size(); i++) {
String token = tokens.get(i);
if (!token.isEmpty()) {
Annotation annotation = Annotation.valueOf(token);
annotations.put(annotation.getName(), annotation);
}
}
return new Segment(id, sequence, annotations.build());
}
}
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