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Optimizing the GATKReportTable.write 

-- Better iteration, caching of strings, better printf calls, to improve the writing performance of GATKReportTables
This commit is contained in:
Mark DePristo 2012-03-27 11:54:35 -04:00
parent 9c384b4813
commit 1f5f737c8b
1 changed files with 11 additions and 13 deletions
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24
public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java
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@ -756,10 +756,6 @@ public class GATKReportTable {
*/
// Get the column widths for everything
HashMap<String, GATKReportColumnFormat> columnFormats = new HashMap<String, GATKReportColumnFormat>();
for (String columnName : columns.keySet()) {
columnFormats.put(columnName, columns.get(columnName).getColumnFormat());
}
String primaryKeyFormat = "%-" + getPrimaryKeyColumnWidth() + "s";
// Emit the table definition
@ -787,7 +783,7 @@ public class GATKReportTable {
if (needsPadding) {
out.printf(" ");
}
out.printf(columnFormats.get(columnName).getNameFormat(), columnName);
out.printf(columns.get(columnName).getColumnFormat().getNameFormat(), columnName);
needsPadding = true;
}
@ -796,29 +792,31 @@ public class GATKReportTable {
out.printf("%n");
// Emit the table body
for (Object primaryKey : primaryKeyColumn) {
for (final Object primaryKey : primaryKeyColumn) {
needsPadding = false;
if (primaryKeyDisplay) {
out.printf(primaryKeyFormat, primaryKey);
needsPadding = true;
}
for (String columnName : columns.keySet()) {
if (columns.get(columnName).isDisplayable()) {
for (final Map.Entry<String, GATKReportColumn> entry : columns.entrySet()) {
final GATKReportColumn column = entry.getValue();
if (column.isDisplayable()) {
if (needsPadding) {
out.printf(" ");
out.print(" ");
}
String value = columns.get(columnName).getStringValue(primaryKey);
out.printf(columnFormats.get(columnName).getValueFormat(), value);
final String value = column.getStringValue(primaryKey);
out.printf(column.getColumnFormat().getValueFormat(), value);
needsPadding = true;
}
}
out.printf("%n");
out.println();
}
out.printf("%n");
out.println();
}
public int getNumRows() {