org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable.XsvTableFeature Maven / Gradle / Ivy
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package org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable;
import htsjdk.tribble.Feature;
import org.broadinstitute.hellbender.exceptions.UserException;
import org.broadinstitute.hellbender.utils.param.ParamUtils;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
/**
* A feature to represent a line in an arbitrarily delimited (XSV) file (i.e. TSV, CSV, etc.).
* Created by jonn on 12/4/17.
*/
public class XsvTableFeature implements Feature {
//==================================================================================================================
// Public Static Members:
//==================================================================================================================
// Private Static Members:
//==================================================================================================================
// Private Members:
/** The column index from which to read the contig for this {@link XsvTableFeature}. */
private final int contigColumn;
/** The column index from which to read the start position for this {@link XsvTableFeature}. */
private final int startColumn;
/** The column index from which to read the end position for this {@link XsvTableFeature}. */
private final int endColumn;
/** The indices for location information in descending order (to be used to remove these columns). */
private final List locationColumnRemoveIndiciesInOrder;
/** Name of the source from which this feature was derived. */
private final String dataSourceName;
/** The contig for this feature. */
private final String contig;
/** The genomic start position for this feature. */
private final int start;
/** The genomic start position for this feature. */
private final int end;
/** The names of the columns in this {@link XsvTableFeature}. */
private final List columnNames;
/** The values for each of the columns in this {@link XsvTableFeature}. */
private final List columnValues;
//==================================================================================================================
// Constructors:
/**
* Create an {@link XsvTableFeature}.
* @param contigColumn The column index from which to read the contig for this {@link XsvTableFeature}.
* @param startColumn The column index from which to read the start position for this {@link XsvTableFeature}.
* @param endColumn The column index from which to read the end position for this {@link XsvTableFeature}.
* @param columnNames The names of the columns in this {@link XsvTableFeature}. Must have same number of entries as {@code columnValues}.
* @param columnValues The values for each of the columns in this {@link XsvTableFeature}. Must have same number of entries as {@code columnNames}.
* @param dataSourceName The name of the source from which this {@link XsvTableFeature} was derived.
*/
public XsvTableFeature(final int contigColumn, final int startColumn, final int endColumn,
final List columnNames, final List columnValues, final String dataSourceName) {
this.contigColumn = contigColumn;
this.startColumn = startColumn;
this.endColumn = endColumn;
this.dataSourceName = dataSourceName;
contig = columnValues.get(contigColumn);
try {
start = Integer.valueOf(columnValues.get(startColumn));
end = Integer.valueOf(columnValues.get(endColumn));
}
catch ( final NumberFormatException ex ) {
throw new UserException.MalformedFile("Could not convert value (" + ex.getMessage() + ") from input file into a number for Data Source: " + dataSourceName);
}
if ( columnNames.size() != columnValues.size() ) {
throw new UserException.BadInput("Number of columns in given header and data do not match: " + columnNames.size() + " != " + columnValues.size());
}
this.columnNames = columnNames;
this.columnValues = columnValues;
// Create our list of indices to remove:
if ( startColumn == endColumn ) {
// Don't add the same column more than once:
locationColumnRemoveIndiciesInOrder = new ArrayList<>(Arrays.asList(contigColumn, startColumn));
}
else {
locationColumnRemoveIndiciesInOrder = new ArrayList<>(Arrays.asList(contigColumn, startColumn, endColumn));
}
locationColumnRemoveIndiciesInOrder.sort(Collections.reverseOrder());
}
//==================================================================================================================
// Override Methods:
@Override
public String getContig() {
return contig;
}
@Override
public int getStart() {
return start;
}
@Override
public int getEnd() {
return end;
}
@Override
public boolean equals(final Object o) {
if ( this == o ) return true;
if ( o == null || getClass() != o.getClass() ) return false;
final XsvTableFeature that = (XsvTableFeature) o;
if ( contigColumn != that.contigColumn ) return false;
if ( startColumn != that.startColumn ) return false;
if ( endColumn != that.endColumn ) return false;
if ( start != that.start ) return false;
if ( end != that.end ) return false;
if ( locationColumnRemoveIndiciesInOrder != null ? !locationColumnRemoveIndiciesInOrder.equals(that.locationColumnRemoveIndiciesInOrder) : that.locationColumnRemoveIndiciesInOrder != null )
return false;
if ( dataSourceName != null ? !dataSourceName.equals(that.dataSourceName) : that.dataSourceName != null )
return false;
if ( contig != null ? !contig.equals(that.contig) : that.contig != null ) return false;
if ( columnNames != null ? !columnNames.equals(that.columnNames) : that.columnNames != null ) return false;
return columnValues != null ? columnValues.equals(that.columnValues) : that.columnValues == null;
}
@Override
public int hashCode() {
int result = contigColumn;
result = 31 * result + startColumn;
result = 31 * result + endColumn;
result = 31 * result + (locationColumnRemoveIndiciesInOrder != null ? locationColumnRemoveIndiciesInOrder.hashCode() : 0);
result = 31 * result + (dataSourceName != null ? dataSourceName.hashCode() : 0);
result = 31 * result + (contig != null ? contig.hashCode() : 0);
result = 31 * result + start;
result = 31 * result + end;
result = 31 * result + (columnNames != null ? columnNames.hashCode() : 0);
result = 31 * result + (columnValues != null ? columnValues.hashCode() : 0);
return result;
}
@Override
public String toString() {
return "XsvTableFeature{" +
"contigColumn=" + contigColumn +
", startColumn=" + startColumn +
", endColumn=" + endColumn +
", locationColumnRemoveIndiciesInOrder=" + locationColumnRemoveIndiciesInOrder +
", dataSourceName='" + dataSourceName + '\'' +
", contig='" + contig + '\'' +
", start=" + start +
", end=" + end +
", columnNames=" + columnNames +
", columnValues=" + columnValues +
'}';
}
//==================================================================================================================
// Static Methods:
//==================================================================================================================
// Instance Methods:
/**
* @return The name of the data source from which this {@link XsvTableFeature} was derived.
*/
public String getDataSourceName() {
return dataSourceName;
}
/**
* Get a value from this {@link XsvTableFeature}.
* @param key The key for the desired value.
* @return The value for the given {@code key}; {@code null} if the given {@code key} is not in this {@link XsvTableFeature}.
*/
public String get(final String key) {
final int position = columnNames.indexOf(key);
if ( position < 0 ) {
return null;
}
return columnValues.get(position);
}
/**
* Get a value from this {@link XsvTableFeature}.
* @param index The index for the desired value. Must be an available index in {@link XsvTableFeature#columnValues}.
* @return The value at the given {@code index}.
*/
public String get(final int index) {
ParamUtils.inRange(index, 0, columnNames.size()-1, "Index out of range: " + index);
return columnValues.get(index);
}
/**
* Get the header from this {@link XsvTableFeature}.
* @return The header for this {@link XsvTableFeature}.
*/
public List getHeader() {
return columnNames;
}
/**
* Get the header from this {@link XsvTableFeature} without the columns that contain location information.
* Specifically the columns specified by the following fields are not included:
* {@link XsvTableFeature#contigColumn}
* {@link XsvTableFeature#startColumn}
* {@link XsvTableFeature#endColumn}
* @return The header for this {@link XsvTableFeature} without location columns.
*/
public List getHeaderWithoutLocationColumns() {
final List outList = new ArrayList<>(columnNames);
for ( final int indx : locationColumnRemoveIndiciesInOrder ) {
outList.remove(indx);
}
return outList;
}
/**
* Get the data from this {@link XsvTableFeature}.
* @return The data for this {@link XsvTableFeature}.
*/
public List getValues() {
return columnValues;
}
/**
* Get the data from this {@link XsvTableFeature} without the columns that contain location information.
* Specifically the columns specified by the following fields are not included:
* {@link XsvTableFeature#contigColumn}
* {@link XsvTableFeature#startColumn}
* {@link XsvTableFeature#endColumn}
* @return The data for this {@link XsvTableFeature} without location columns.
*/
public List getValuesWithoutLocationColumns() {
final List outList = new ArrayList<>(columnValues);
for ( final int indx : locationColumnRemoveIndiciesInOrder ) {
outList.remove(indx);
}
return outList;
}
/**
* @return The number of entries in this {@link XsvTableFeature}.
*/
public int size() {
return columnValues.size();
}
//==================================================================================================================
// Helper Data Types:
}
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