package picard.util;
import htsjdk.samtools.util.CloseableIterator;
import picard.PicardException;
import java.util.Collections;
import java.util.HashMap;
import java.util.Map;
import java.util.NoSuchElementException;
import java.util.Set;
/**
* Iterate through a delimited text file in which columns are found by looking at a header line rather than by position.
*
* TODO: This effectively replaces TabbedTextFileWithHeaderParser although the latter hasn't been modified to use this
* code instead.
*
* @author jgentry@broadinstitute.org
*/
public class DelimitedTextFileWithHeaderIterator implements CloseableIterator<DelimitedTextFileWithHeaderIterator.Row> {
public class Row {
private final String[] fields;
private final String currentLine;
Row(final String[] fields, final String source) {
this.fields = fields;
this.currentLine = source;
}
/**
* @return Array of fields in the order they appear in the file.
*/
public String[] getFields() {
return fields;
}
public String getField(final String columnLabel) {
final Integer key = columnLabelIndices.get(columnLabel);
if (key == null) throw new NoSuchElementException(String.format("column %s in %s", columnLabel, parser.getFileName()));
return fields[key];
}
public Integer getIntegerField(final String columnLabel) {
if (fields[columnLabelIndices.get(columnLabel)] == null) return null;
return Integer.parseInt(fields[columnLabelIndices.get(columnLabel)]);
}
public String getCurrentLine() {
return this.currentLine;
}
}
/**
* Map from column label to positional index.
*/
private final Map<String, Integer> columnLabelIndices = new HashMap<String, Integer>();
private final BasicInputParser parser;
public DelimitedTextFileWithHeaderIterator(final BasicInputParser parser) {
this.parser = parser;
if (!parser.hasNext()) {
throw new PicardException("No header line found in file " + parser.getFileName());
}
final String[] columnLabels = parser.next();
for (int i = 0; i < columnLabels.length; ++i) {
columnLabelIndices.put(columnLabels[i], i);
}
}
/**
* @param columnLabel
* @return True if the given column label appears in the header.
*/
public boolean hasColumn(final String columnLabel) {
return columnLabelIndices.containsKey(columnLabel);
}
/**
*
* @return The set of column labels for this file in no particular order.
*/
public Set<String> columnLabels() {
return columnLabelIndices.keySet();
}
public int getCurrentLineNumber() {
return parser.getCurrentLineNumber();
}
public Set<String> getColumnNames() {
return Collections.unmodifiableSet(this.columnLabelIndices.keySet());
}
@Override
public boolean hasNext() {
return parser.hasNext();
}
@Override
public Row next() {
final String[] fields = parser.next();
final String source = parser.getCurrentLine();
return new Row(fields, source);
}
@Override
public void remove() {
throw new UnsupportedOperationException();
}
@Override
public void close() {
parser.close();
}
}