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Now supports a mode where the primary key isn't sorted. In this case the records are displayed in the order in which they are added to to the table.

This commit is contained in:
Mark DePristo 2011-07-18 15:40:15 -04:00
parent 6d5e87da10
commit 45702d3084
2 changed files with 17 additions and 15 deletions
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6
public/java/src/org/broadinstitute/sting/gatk/report/GATKReport.java
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@ -100,7 +100,11 @@ public class GATKReport {
* @param tableDescription the description of the table
*/
public void addTable(String tableName, String tableDescription) {
GATKReportTable table = new GATKReportTable(tableName, tableDescription);
addTable(tableName, tableDescription, true);
}
public void addTable(String tableName, String tableDescription, boolean sortByPrimaryKey) {
GATKReportTable table = new GATKReportTable(tableName, tableDescription, sortByPrimaryKey);
tables.put(tableName, table);
}

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

@ -3,9 +3,7 @@ package org.broadinstitute.sting.gatk.report;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.io.PrintStream;
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.TreeSet;
import java.util.*;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
@ -96,8 +94,9 @@ public class GATKReportTable {
private String tableDescription;
private String primaryKeyName;
private TreeSet<Object> primaryKeyColumn;
private Collection<Object> primaryKeyColumn;
private boolean primaryKeyDisplay;
boolean sortByPrimaryKey = true;
private LinkedHashMap<String, GATKReportColumn> columns;
@ -121,12 +120,17 @@ public class GATKReportTable {
* @param tableDescription the description of the table
*/
public GATKReportTable(String tableName, String tableDescription) {
if (!isValidName(tableName)) {
this(tableName, tableDescription, true);
}
public GATKReportTable(String tableName, String tableDescription, boolean sortByPrimaryKey) {
if (!isValidName(tableName)) {
throw new ReviewedStingException("Attempted to set a GATKReportTable name of '" + tableName + "'. GATKReportTable names must be purely alphanumeric - no spaces or special characters are allowed.");
}
this.tableName = tableName;
this.tableDescription = tableDescription;
this.sortByPrimaryKey = sortByPrimaryKey;
columns = new LinkedHashMap<String, GATKReportColumn>();
}
@ -137,20 +141,14 @@ public class GATKReportTable {
* @param primaryKeyName the name of the primary key column
*/
public void addPrimaryKey(String primaryKeyName) {
if (!isValidName(primaryKeyName)) {
throw new ReviewedStingException("Attempted to set a GATKReportTable primary key name of '" + primaryKeyName + "'. GATKReportTable primary key names must be purely alphanumeric - no spaces or special characters are allowed.");
}
this.primaryKeyName = primaryKeyName;
primaryKeyColumn = new TreeSet<Object>();
primaryKeyDisplay = true;
addPrimaryKey(primaryKeyName, true);
}
/**
* Add an optionally visible primary key column. This becomes the unique identifier for every column in the table, and will always be printed as the first column.
*
* @param primaryKeyName the name of the primary key column
* @param display should this primary key be displayed?
*/
public void addPrimaryKey(String primaryKeyName, boolean display) {
if (!isValidName(primaryKeyName)) {
@ -159,7 +157,7 @@ public class GATKReportTable {
this.primaryKeyName = primaryKeyName;
primaryKeyColumn = new TreeSet<Object>();
primaryKeyColumn = sortByPrimaryKey ? new TreeSet<Object>() : new LinkedList<Object>();
primaryKeyDisplay = display;
}