/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.nbio.sequencing.io.fastq;
/**
* Fluent builder API for creating FASTQ formatted sequences.
*
* @since 3.0.3
*/
public final class FastqBuilder
{
/** Description for this FASTQ formatted sequence builder. */
private String description;
/** Sequence for this FASTQ formatted sequence builder. */
private StringBuilder sequence;
/** Quality scores for this FASTQ formatted sequence builder. */
private StringBuilder quality;
/** FASTQ sequence format variant for this FASTQ formatted sequence builder. */
private FastqVariant variant = DEFAULT_VARIANT;
/** Default FASTQ sequence format variant, <code>FastqVariant.FASTQ_SANGER</code>. */
public static final FastqVariant DEFAULT_VARIANT = FastqVariant.FASTQ_SANGER;
/**
* Create a new FASTQ formatted sequence builder.
*/
public FastqBuilder()
{
// empty
}
/**
* Return the description for this FASTQ formatted sequence builder.
*
* @return the description for this FASTQ formatted sequence builder
*/
public String getDescription()
{
return description;
}
/**
* Return this FASTQ formatted sequence builder configured with the specified description.
*
* @param description description for this FASTQ formatted sequence builder, must not be null
* @return this FASTQ formatted sequence builder configured with the specified description
*/
public FastqBuilder withDescription(final String description)
{
if (description == null)
{
throw new IllegalArgumentException("description must not be null");
}
this.description = description;
return this;
}
/**
* Return this FASTQ formatted sequence builder configured with the specified sequence.
*
* @param sequence sequence for this FASTQ formatted sequence builder, must not be null
* @return this FASTQ formatted sequence builder configured with the specified sequence
*/
public FastqBuilder withSequence(final String sequence)
{
if (sequence == null)
{
throw new IllegalArgumentException("sequence must not be null");
}
if (this.sequence == null)
{
this.sequence = new StringBuilder(sequence.length());
}
this.sequence.replace(0, this.sequence.length(), sequence);
return this;
}
/**
* Return this FASTQ formatted sequence builder configured with the specified sequence
* appended to its current sequence.
*
* @param sequence sequence to append to the sequence for this FASTQ formatted sequence builder, must not be null
* @return this FASTQ formatted sequence builder configured with the specified sequence
* appended to its current sequence
*/
public FastqBuilder appendSequence(final String sequence)
{
if (sequence == null)
{
throw new IllegalArgumentException("sequence must not be null");
}
if (this.sequence == null)
{
this.sequence = new StringBuilder(sequence.length());
}
this.sequence.append(sequence);
return this;
}
/**
* Return this FASTQ formatted sequence builder configured with the specified quality scores.
*
* @param quality quality scores for this FASTQ formatted sequence builder, must not be null
* @return this FASTQ formatted sequence builder configured with the specified quality scores
*/
public FastqBuilder withQuality(final String quality)
{
if (quality == null)
{
throw new IllegalArgumentException("quality must not be null");
}
if (this.quality == null)
{
this.quality = new StringBuilder(quality.length());
}
this.quality.replace(0, this.quality.length(), quality);
return this;
}
/**
* Return this FASTQ formatted sequence builder configured with the specified quality scores
* appended to its current quality scores.
*
* @param quality quality scores to append to the quality scores for this FASTQ formatted sequence
* builder, must not be null
* @return this FASTQ formatted sequence builder configured with the specified quality scores
* appended to its current quality scores
*/
public FastqBuilder appendQuality(final String quality)
{
if (quality == null)
{
throw new IllegalArgumentException("quality must not be null");
}
if (this.quality == null)
{
this.quality = new StringBuilder(quality.length());
}
this.quality.append(quality);
return this;
}
/**
* Return true if the sequence and quality scores for this FASTQ formatted sequence builder are equal in length.
*
* @return true if the sequence and quality scores for this FASTQ formatted sequence builder are equal in length
*/
public boolean sequenceAndQualityLengthsMatch()
{
if (sequence == null && quality == null)
{
return true;
}
if ((sequence != null && quality == null) || (sequence == null && quality != null))
{
return false;
}
return sequence.length() == quality.length();
}
/**
* Return this FASTQ formatted sequence builder configured with the specified FASTQ sequence format variant.
*
* @param variant FASTQ sequence format variant for this FASTQ formatted sequence builder, must not be null
* @return this FASTQ formatted sequence builder configured with the specified FASTQ sequence format variant
*/
public FastqBuilder withVariant(final FastqVariant variant)
{
if (variant == null)
{
throw new IllegalArgumentException("variant must not be null");
}
this.variant = variant;
return this;
}
/**
* Build and return a new FASTQ formatted sequence configured from the properties of this builder.
*
* @return a new FASTQ formatted sequence configured from the properties of this builder
* @throws IllegalStateException if the configuration of this builder results in an illegal state
*/
public Fastq build()
{
if (description == null)
{
throw new IllegalStateException("description must not be null");
}
if (sequence == null)
{
throw new IllegalStateException("sequence must not be null");
}
if (quality == null)
{
throw new IllegalStateException("quality must not be null");
}
if (!sequenceAndQualityLengthsMatch())
{
throw new IllegalStateException("sequence and quality scores must be the same length");
}
Fastq fastq = new Fastq(description, sequence.toString(), quality.toString(), variant);
return fastq;
}
}