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GATKReportTable output refactor 

writing out a GATKReportTable was O(n^2)!!!!!
New implementation is O(n). What a difference, when N = 2^16...
This commit is contained in:
Mauricio Carneiro 2012-03-28 16:56:40 -04:00
parent 5ff24f8cf3
commit 8f0e9d74ce
2 changed files with 50 additions and 41 deletions
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65
public/java/src/org/broadinstitute/sting/gatk/report/GATKReportColumn.java
View File

@ -26,7 +26,9 @@ package org.broadinstitute.sting.gatk.report;
import org.apache.commons.lang.math.NumberUtils;
import java.util.*;
import java.util.Arrays;
import java.util.Collection;
import java.util.LinkedHashMap;
/**
* Holds values for a column in a GATK report table
@ -38,6 +40,10 @@ public class GATKReportColumn extends LinkedHashMap<Object, Object> {
final private boolean display;
final private GATKReportDataType dataType;
private GATKReportColumnFormat columnFormat;
private GATKReportColumnFormat.Alignment alignment = GATKReportColumnFormat.Alignment.RIGHT; // default alignment is to the right unless values added ask for a left alignment
private int maxWidth = 0;
/**
* Construct the column object, specifying the column name, default value, whether or not the column should be
* displayed, and the format string. This cannot be null.
@ -49,6 +55,7 @@ public class GATKReportColumn extends LinkedHashMap<Object, Object> {
*/
public GATKReportColumn(String columnName, Object defaultValue, boolean display, String format) {
this.columnName = columnName;
this.maxWidth = columnName.length();
this.display = display;
if ( format.equals("") ) {
this.format = "%s";
@ -85,7 +92,8 @@ public class GATKReportColumn extends LinkedHashMap<Object, Object> {
/**
* Return an object from the column, but if it doesn't exist, return the default value. This is useful when writing
* tables, as the table gets written properly without having to waste storage for the unset elements (usually the zero
* tables, as the table gets written properly without having to waste storage for the unset elements (usually the
* zero
* values) in the table.
*
* @param primaryKey the primary key position in the column that should be retrieved
@ -120,32 +128,17 @@ public class GATKReportColumn extends LinkedHashMap<Object, Object> {
}
/**
* Get the display width for this column. This allows the entire column to be displayed with the appropriate, fixed width.
* Get the display width for this column. This allows the entire column to be displayed with the appropriate, fixed
* width.
*
* @return the format string for this column
*/
public GATKReportColumnFormat getColumnFormat() {
int maxWidth = columnName.length();
GATKReportColumnFormat.Alignment alignment = GATKReportColumnFormat.Alignment.RIGHT;
if (columnFormat != null)
return columnFormat;
for (Object obj : this.values()) {
if (obj != null) {
String formatted = formatValue(obj);
int width = formatted.length();
if (width > maxWidth) {
maxWidth = width;
}
if (alignment == GATKReportColumnFormat.Alignment.RIGHT) {
if (!isRightAlign(formatted)) {
alignment = GATKReportColumnFormat.Alignment.LEFT;
}
}
}
}
return new GATKReportColumnFormat(maxWidth, alignment);
columnFormat = new GATKReportColumnFormat(maxWidth, alignment);
return columnFormat;
}
private static final Collection<String> RIGHT_ALIGN_STRINGS = Arrays.asList(
@ -176,10 +169,11 @@ public class GATKReportColumn extends LinkedHashMap<Object, Object> {
String value;
if (obj == null) {
value = "null";
} else if ( dataType.equals(GATKReportDataType.Unknown) &&
(obj instanceof Double || obj instanceof Float) ) {
}
else if ( dataType.equals(GATKReportDataType.Unknown) && (obj instanceof Double || obj instanceof Float) ) {
value = String.format("%.8f", obj);
} else
}
else
value = String.format(format, obj);
return value;
@ -226,4 +220,23 @@ public class GATKReportColumn extends LinkedHashMap<Object, Object> {
else
return format;
}
@Override
public Object put(Object key, Object value) {
if (value != null) {
String formatted = formatValue(value);
updateMaxWidth(formatted);
updateFormat(formatted);
}
return super.put(key, value);
}
private void updateMaxWidth(String formatted) {
maxWidth = Math.max(formatted.length(), maxWidth);
}
private void updateFormat(String formatted) {
if (!isRightAlign(formatted))
alignment = GATKReportColumnFormat.Alignment.LEFT;
}
}

26
public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java
View File

@ -405,7 +405,7 @@ public class GATKReportTable {
public void set(Object primaryKey, String columnName, Object value) {
verifyEntry(primaryKey, columnName);
GATKReportColumn column = columns.get(columnName);
// Check if value is of same type as column
//todo -- Check if value is of same type as column
// We do not accept internal null values
if (value == null)
@ -422,17 +422,18 @@ public class GATKReportTable {
try {
newValue = Long.parseLong((String) value);
} catch (Exception e) {
/** do nothing */
}
}
if (column.getDataType().equals(GATKReportDataType.Decimal)) {
try {
newValue = Double.parseDouble((String) value);
} catch (Exception e) {
/** do nothing */
}
}
if (column.getDataType().equals(GATKReportDataType.Character) && ((String) value).length() == 1) {
newValue = ((String) value).charAt(0);
}
}
@ -900,13 +901,10 @@ public class GATKReportTable {
public boolean isSameFormat(GATKReportTable table) {
//Should we add the sortByPrimaryKey as a check?
if (!columns.isSameFormat(table.columns)) {
return false;
}
return (primaryKeyDisplay == table.primaryKeyDisplay &&
primaryKeyName.equals(table.primaryKeyName) &&
tableName.equals(table.tableName) &&
tableDescription.equals(table.tableDescription));
return columns.isSameFormat(table.columns) &&
(primaryKeyDisplay == table.primaryKeyDisplay && primaryKeyName.equals(table.primaryKeyName) &&
tableName.equals(table.tableName) &&
tableDescription.equals(table.tableDescription));
}
/**
@ -916,12 +914,10 @@ public class GATKReportTable {
* @return true if all field in the reports, tables, and columns are equal.
*/
public boolean equals(GATKReportTable table) {
if (!isSameFormat(table)) {
return false;
}
return (columns.equals(table.columns) &&
primaryKeyColumn.equals(table.primaryKeyColumn) &&
sortByPrimaryKey == table.sortByPrimaryKey);
return isSameFormat(table) &&
(columns.equals(table.columns) &&
primaryKeyColumn.equals(table.primaryKeyColumn) &&
sortByPrimaryKey == table.sortByPrimaryKey);
}
}