/**
* Handle writing the {@link PerSequenceQualityScores} to the database.
*
* @param scores the {@link PerSequenceQualityScores} computed by fastqc.
* @param analysis the {@link AnalysisFastQCBuilder} to update.
*/
private void handlePerSequenceQualityScores(
PerSequenceQualityScores scores, AnalysisFastQCBuilder analysis) throws IOException {
ByteArrayOutputStream os = new ByteArrayOutputStream();
LineGraph lg = (LineGraph) scores.getResultsPanel();
BufferedImage b = new BufferedImage(800, 600, BufferedImage.TYPE_INT_RGB);
Graphics g = b.getGraphics();
lg.paint(g, b.getWidth(), b.getHeight());
ImageIO.write(b, "PNG", os);
byte[] image = os.toByteArray();
analysis.perSequenceQualityScoreChart(image);
}
/**
* Handle writing the {@link DuplicationLevel} to the database.
*
* @param duplicationLevel the {@link DuplicationLevel} calculated by fastqc.
* @param analysis the {@link AnalysisFastQCBuilder} to update.
*/
private void handleDuplicationLevel(
DuplicationLevel duplicationLevel, AnalysisFastQCBuilder analysis) throws IOException {
ByteArrayOutputStream os = new ByteArrayOutputStream();
LineGraph lg = (LineGraph) duplicationLevel.getResultsPanel();
BufferedImage b = new BufferedImage(800, 600, BufferedImage.TYPE_INT_RGB);
Graphics g = b.getGraphics();
lg.paint(g, b.getWidth(), b.getHeight());
ImageIO.write(b, "PNG", os);
byte[] image = os.toByteArray();
analysis.duplicationLevelChart(image);
}
/**
* Handle writing the {@link BasicStats} to the database.
*
* @param stats the {@link BasicStats} computed by fastqc.
* @param analysis the {@link AnalysisFastQCBuilder} to update.
*/
private void handleBasicStats(BasicStats stats, AnalysisFastQCBuilder analysis) {
analysis.fileType(stats.getFileType());
analysis.encoding(PhredEncoding.getFastQEncodingOffset(stats.getLowestChar()).name());
analysis.minLength(stats.getMinLength());
analysis.maxLength(stats.getMaxLength());
analysis.totalSequences(stats.getActualCount());
analysis.filteredSequences(stats.getFilteredCount());
analysis.gcContent(stats.getGCContent());
analysis.totalBases(
stats.getACount()
+ stats.getGCount()
+ stats.getCCount()
+ stats.getTCount()
+ stats.getNCount());
}