/*
* The MIT License
*
* Copyright (c) 2009 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package htsjdk.samtools;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
/**
* In-memory representation of @PG SAM header record.
*/
public class SAMProgramRecord extends AbstractSAMHeaderRecord {
public static final String PROGRAM_GROUP_ID_TAG = "ID";
public static final String PROGRAM_NAME_TAG = "PN";
public static final String PROGRAM_VERSION_TAG = "VN";
public static final String COMMAND_LINE_TAG = "CL";
public static final String PREVIOUS_PROGRAM_GROUP_ID_TAG = "PP";
private String mProgramGroupId;
public static final Set<String> STANDARD_TAGS = Collections.unmodifiableSet(
new HashSet<String>(Arrays.asList(PROGRAM_GROUP_ID_TAG,
PROGRAM_NAME_TAG,
PROGRAM_VERSION_TAG,
COMMAND_LINE_TAG,
PREVIOUS_PROGRAM_GROUP_ID_TAG)) );
public SAMProgramRecord(final String programGroupId) {
this.mProgramGroupId = programGroupId;
}
public SAMProgramRecord(final String id, SAMProgramRecord srcProgramRecord) {
mProgramGroupId = id;
for (final Map.Entry<String, String> entry : srcProgramRecord.getAttributes()) {
setAttribute(entry.getKey(), entry.getValue());
}
}
public String getId() {
return getProgramGroupId();
}
public String getProgramGroupId() {
return mProgramGroupId;
}
public String getProgramName() {
return (String)getAttribute(PROGRAM_NAME_TAG);
}
public void setProgramName(final String name) {
setAttribute(PROGRAM_NAME_TAG, name);
}
public String getProgramVersion() {
return (String)getAttribute(PROGRAM_VERSION_TAG);
}
public void setProgramVersion(final String version) {
setAttribute(PROGRAM_VERSION_TAG, version);
}
public String getCommandLine() {
return (String)getAttribute(COMMAND_LINE_TAG);
}
public void setCommandLine(final String commandLine) {
setAttribute(COMMAND_LINE_TAG, commandLine);
}
public String getPreviousProgramGroupId() {
return (String)getAttribute(PREVIOUS_PROGRAM_GROUP_ID_TAG);
}
public void setPreviousProgramGroupId(final String id) {
setAttribute(PREVIOUS_PROGRAM_GROUP_ID_TAG, id);
}
/**
* @return true if this == that except for the program group ID, which is arbitrary
*/
public boolean equivalent(final SAMProgramRecord that) {
return attributesEqual(that);
}
@Override
public boolean equals(final Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
final SAMProgramRecord that = (SAMProgramRecord) o;
if (!attributesEqual(that)) return false;
if (mProgramGroupId != null ? !mProgramGroupId.equals(that.mProgramGroupId) : that.mProgramGroupId != null) return false;
return true;
}
@Override
public int hashCode() {
int result = mProgramGroupId != null ? mProgramGroupId.hashCode() : 0;
result = 31 * result + attributesHashCode();
return result;
}
Set<String> getStandardTags() {
return STANDARD_TAGS;
}
}