Java tutorial
/* dsh-bio-assembly Assemblies. Copyright (c) 2013-2019 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 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.assembly.gfa.Reference; import org.dishevelled.bio.assembly.gfa.Tag; /** * 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 tags tags, 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<String, Tag> tags) { super(tags); 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, getTags()); } /** * Return the identifier for this gap, if any. * * @return the identifier for this gap, if any */ public String getId() { return 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 the variance for this gap, if any. * * @return the variance for this gap, if any */ public Integer getVariance() { return variance; } @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(getTags(), g.getTags()); } @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 (!getTags().isEmpty()) { sb.append("\t"); joiner.appendTo(sb, getTags().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"), "value must start with G"); List<String> tokens = Splitter.on("\t").splitToList(value); if (tokens.size() < 6) { throw new IllegalArgumentException("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<String, Tag> tags = ImmutableMap.builder(); for (int i = 6; i < tokens.size(); i++) { Tag tag = Tag.valueOf(tokens.get(i)); tags.put(tag.getName(), tag); } return new Gap(id, source, target, distance, variance, tags.build()); } }