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; /** * 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 tags tags, 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<String, Tag> tags) { super(tags); 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, getTags()); } /** * 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 the alignment for this fragment, if any. * * @return the alignment for this fragment, if any */ public Alignment getAlignment() { return alignment; } @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(getTags(), f.getTags()); } @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 (!getTags().isEmpty()) { sb.append("\t"); joiner.appendTo(sb, getTags().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"), "value must start with F"); List<String> tokens = Splitter.on("\t").splitToList(value); if (tokens.size() < 8) { throw new IllegalArgumentException("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<String, Tag> tags = ImmutableMap.builder(); for (int i = 8; i < tokens.size(); i++) { Tag tag = Tag.valueOf(tokens.get(i)); tags.put(tag.getName(), tag); } return new Fragment(segmentId, external, segmentStart, segmentEnd, fragmentStart, fragmentEnd, alignment, tags.build()); } }