org.broadinstitute.hellbender.utils.report

Class GATKReportTable

java.lang.Object

org.broadinstitute.hellbender.utils.report.GATKReportTable

public final class GATKReportTable
extends java.lang.Object

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	GATKReportTable.Sorting
protected static class	GATKReportTable.TableDataHeaderFields
protected static class	GATKReportTable.TableNameHeaderFields

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	INVALID_TABLE_NAME_REGEX REGEX that matches any table with an invalid name

Constructor Summary

Constructors

Constructor and Description
GATKReportTable(java.io.BufferedReader reader, GATKReportVersion version) Construct a new GATK report table from the reader Note that the row ID mappings are just the index -> index
GATKReportTable(java.lang.String tableName, java.lang.String tableDescription, int numColumns) Construct a new GATK report table with the specified name and description Sorting will be done with GATKReportTable.Sorting.SORT_BY_ROW
GATKReportTable(java.lang.String tableName, java.lang.String tableDescription, int numColumns, GATKReportTable.Sorting sortingWay) Construct a new GATK report table with the specified name and description and whether to sort rows by the row ID.

Method Summary

Modifier and Type	Method and Description
void	addColumn(java.lang.String columnName, java.lang.String format) Add a column to the report and the format string used to display the data.
void	addRowID(java.lang.String ID, boolean populateFirstColumn) Add a mapping from ID to the index of a new row added to the table.
void	addRowIDMapping(java.lang.Object ID, int index, boolean populateFirstColumn) Add a mapping from ID to row index.
void	addRowIDMapping(java.lang.String ID, int index) Add a mapping from ID to row index.
void	concat(GATKReportTable table) Concatenates the rows from the table to this one
boolean	equals(GATKReportTable table) Checks that the tables are exactly the same.
java.lang.Object	get(int rowIndex, int columnIndex) Get a value from the given position in the table
java.lang.Object	get(int rowIndex, java.lang.String columnName) Get a value from the given position in the table
java.lang.Object	get(java.lang.Object rowID, java.lang.String columnName) Get a value from the given position in the table
java.util.List<GATKReportColumn>	getColumnInfo()
int	getNumColumns()
int	getNumRows()
java.lang.Object[]	getRow(int rowIndex) Get entire row from the given row index in the table
java.lang.String	getTableDescription()
java.lang.String	getTableName()
void	increment(java.lang.Object rowID, java.lang.String columnName) Increment the value for a given position in the table.
boolean	isSameFormat(GATKReportTable table) Returns whether or not the two tables have the same format including columns and everything in between.
void	set(int rowIndex, int colIndex, java.lang.Object value) Set the value for a given position in the table.
void	set(java.lang.Object rowID, java.lang.String columnName, java.lang.Object value) Set the value for a given position in the table.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

INVALID_TABLE_NAME_REGEX

public static final java.lang.String INVALID_TABLE_NAME_REGEX

REGEX that matches any table with an invalid name

See Also:

Constant Field Values

Constructor Detail

GATKReportTable

public GATKReportTable(java.io.BufferedReader reader,
                       GATKReportVersion version)

Construct a new GATK report table from the reader Note that the row ID mappings are just the index -> index

Parameters:

reader - the reader

version - the GATK report version

GATKReportTable

public GATKReportTable(java.lang.String tableName,
                       java.lang.String tableDescription,
                       int numColumns)

Construct a new GATK report table with the specified name and description Sorting will be done with GATKReportTable.Sorting.SORT_BY_ROW

Parameters:

tableName - the name of the table

tableDescription - the description of the table

numColumns - the number of columns in this table

GATKReportTable

public GATKReportTable(java.lang.String tableName,
                       java.lang.String tableDescription,
                       int numColumns,
                       GATKReportTable.Sorting sortingWay)

Construct a new GATK report table with the specified name and description and whether to sort rows by the row ID.

Parameters:

tableName - the name of the table

tableDescription - the description of the table

numColumns - the number of columns in this table

sortingWay - in what way to sort rows (instead of the order in which they were added)

Method Detail

addRowID

public void addRowID(java.lang.String ID,
                     boolean populateFirstColumn)

Add a mapping from ID to the index of a new row added to the table.

Parameters:

ID - the unique ID

populateFirstColumn - should we automatically populate the first column with the row's ID?

addRowIDMapping

public void addRowIDMapping(java.lang.String ID,
                            int index)

Add a mapping from ID to row index.

Parameters:

ID - the unique ID

index - the index associated with the ID

addRowIDMapping

public void addRowIDMapping(java.lang.Object ID,
                            int index,
                            boolean populateFirstColumn)

Add a mapping from ID to row index.

Parameters:

ID - the unique ID

index - the index associated with the ID

populateFirstColumn - should we automatically populate the first column with the row's ID?

addColumn

public void addColumn(java.lang.String columnName,
                      java.lang.String format)

Add a column to the report and the format string used to display the data.

Parameters:

columnName - the name of the column

format - the format string used to display data

set

public void set(java.lang.Object rowID,
                java.lang.String columnName,
                java.lang.Object value)

Set the value for a given position in the table. If the row ID doesn't exist, it will create a new row in the table with the given ID.

Parameters:

rowID - the row ID

columnName - the name of the column

value - the value to set

set

public void set(int rowIndex,
                int colIndex,
                java.lang.Object value)

Set the value for a given position in the table. If the row index doesn't exist, it will create new rows in the table accordingly.

Parameters:

rowIndex - the row index

colIndex - the column index

value - the value to set

increment

public void increment(java.lang.Object rowID,
                      java.lang.String columnName)

Increment the value for a given position in the table. Throws an exception if the value in the cell is not an integer.

Parameters:

rowID - the row ID

columnName - the name of the column

get

public java.lang.Object get(java.lang.Object rowID,
                            java.lang.String columnName)

Get a value from the given position in the table

Parameters:

rowID - the row ID

columnName - the name of the column

Returns:

the value stored at the specified position in the table

getRow

public java.lang.Object[] getRow(int rowIndex)

Get entire row from the given row index in the table

Parameters:

rowIndex - the index of the column

Returns:

the entire row at the specified index

get

public java.lang.Object get(int rowIndex,
                            java.lang.String columnName)

Get a value from the given position in the table

Parameters:

rowIndex - the row ID

columnName - the name of the column

Returns:

the value stored at the specified position in the table

get

public java.lang.Object get(int rowIndex,
                            int columnIndex)

Get a value from the given position in the table

Parameters:

rowIndex - the index of the row

columnIndex - the index of the column

Returns:

the value stored at the specified position in the table

getNumRows

public int getNumRows()

Returns:

The number of rows in this table

getNumColumns

public int getNumColumns()

Returns:

The number of columns in this table

getColumnInfo

public java.util.List<GATKReportColumn> getColumnInfo()

Returns:

A list of GATKReportColumn objects describing this table

getTableName

public java.lang.String getTableName()

Returns:

The name of this table

getTableDescription

public java.lang.String getTableDescription()

Returns:

The description for this table

concat

public void concat(GATKReportTable table)

Concatenates the rows from the table to this one

Parameters:

table - another GATK table

isSameFormat

public boolean isSameFormat(GATKReportTable table)

Returns whether or not the two tables have the same format including columns and everything in between. This does not check if the data inside is the same. This is the check to see if the two tables are gatherable or reduceable

Parameters:

table - another GATK table

Returns:

true if the the tables are gatherable

equals

public boolean equals(GATKReportTable table)

Checks that the tables are exactly the same.

Parameters:

table - another GATK report

Returns:

true if all field in the reports, tables, and columns are equal.