package org.broad.igv.util.blat;
import org.broad.igv.feature.PSLRecord;
import org.broad.igv.feature.Strand;
import javax.swing.table.AbstractTableModel;
import java.io.*;
import java.util.List;
/**
* Table model for Blat results (psl records)
* <p/>
* tChr tStart tEnd strand score match misMatch repMatcch Ns qGapCount qGapBases tGapCount tGapBases
*
* @author jrobinso
* Date: 11/29/12
* Time: 6:46 PM
*/
public class BlatTableModel extends AbstractTableModel {
String[] columnNames = {"chr", "start", "end", "strand", "score", "match", "mis-match", "rep. match", "N's",
"Q gap count", "Q gap bases", "T gap count", "T gap bases"};
List<PSLRecord> records;
public BlatTableModel(List<PSLRecord> records) {
this.records = records;
}
@Override
public int getRowCount() {
return records.size(); //To change body of implemented methods use File | Settings | File Templates.
}
@Override
public int getColumnCount() {
return columnNames.length; //To change body of implemented methods use File | Settings | File Templates.
}
@Override
public String getColumnName(int col) {
return columnNames[col];
}
@Override
public Object getValueAt(int rowIndex, int columnIndex) {
PSLRecord record = records.get(rowIndex);
switch (columnIndex) {
case 0:
return record.getChr();
case 1:
return record.getStart();
case 2:
return record.getEnd();
case 3:
return (record.getStrand() == Strand.POSITIVE ? "+" : "-");
case 4:
return (int) record.getScore();
case 5:
return record.getMatch();
case 6:
return record.getMisMatch();
case 7:
return record.getRepMatch();
case 8:
return record.getNs();
case 9:
return record.getQGapCount();
case 10:
return record.getQGapBases();
case 11:
return record.getTGapCount();
case 12:
return record.getTGapBases();
default:
return "?";
}
}
public String getChr(int rowIndex) {
PSLRecord record = records.get(rowIndex);
return record.getChr();
}
public int getStart(int rowIndex) {
PSLRecord record = records.get(rowIndex);
return record.getStart();
}
public int getEnd(int rowIndex) {
PSLRecord record = records.get(rowIndex);
return record.getEnd();
}
public void save(File f) throws IOException {
PrintWriter pw = null;
try {
pw = new PrintWriter(new BufferedWriter(new FileWriter(f)));
for (PSLRecord record : records) {
pw.println(record.getText());
}
} finally {
if (pw != null) pw.close();
}
}
}