TableColumnCollection (gatk 4.1.4.1 API)

java.lang.Object
- org.broadinstitute.hellbender.utils.tsv.TableColumnCollection

public final class TableColumnCollection
extends java.lang.Object

Represents a list of table columns.

Constructor Summary

Constructors
Constructor and Description
`TableColumnCollection(java.lang.Class<? extends java.lang.Enum<?>> enumClass)` Creates a new table-column collection from a set of enum constants.
`TableColumnCollection(java.lang.Iterable<java.lang.String> names)` Creates a new table-column names collection.
`TableColumnCollection(java.lang.Object... names)` Creates a new table-column names collection.
`TableColumnCollection(java.lang.String... names)` Creates a new table-column names collection.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`static java.lang.String[]`	`checkNames(java.lang.Object[] columnNames, java.util.function.Function<java.lang.String,java.lang.RuntimeException> exceptionFactory)` Checks that a column name, as objects, array is valid.
`static java.lang.String[]`	`checkNames(java.lang.String[] columnNames, java.util.function.Function<java.lang.String,java.lang.RuntimeException> exceptionFactory)` Checks that a column name array is valid.
`int`	`columnCount()` Returns the number of columns.
`boolean`	`contains(java.lang.String name)` Check whether there is such a column by name.
`boolean`	`containsAll(java.lang.Iterable<java.lang.String> names)` Checks whether columns contain all the names in an array.
`boolean`	`containsAll(java.lang.String... names)` Checks whether columns contain all the names in an array.
`boolean`	`containsExactly(java.lang.String... names)` Checks whether columns contain all the names in an array and no other.
`boolean`	`equals(java.lang.Object o)`
`int`	`hashCode()`
`int`	`indexOf(java.lang.String name)` Returns the index of a column by its name.
`boolean`	`matches(int index, java.lang.String name)` Checks a column names matches given one.
`boolean`	`matchesAll(int offset, java.lang.String... names)` Checks an array of column matches the column names starting from a given index.
`boolean`	`matchesExactly(java.lang.String... names)` Checks whether columns contain all the names in an array and no other and in the very same order.
`java.lang.String`	`nameAt(int index)` Returns the name of a column by its index.
`java.util.List<java.lang.String>`	`names()` Returns the column names ordered by column index.

Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - TableColumnCollection
```
public TableColumnCollection(java.lang.Iterable<java.lang.String> names)
```
    Creates a new table-column names collection.
    The new instance will have its own copy of the input name array, thus is safe to modify such an array after calling this constructor; it won't modify the state of this object.
    
    Parameters:
    
    names - the column names.
    
    Throws:
    
    java.lang.IllegalArgumentException - if names is not a valid column name iterable of names as determined by checkNames.
  - TableColumnCollection
```
public TableColumnCollection(java.lang.String... names)
```
    Creates a new table-column names collection.
    The new instance will have its own copy of the input name array, thus is safe to modify such an array after calling this constructor; it won't modify the state of this object.
    
    Parameters:
    
    names - the column names.
    
    Throws:
    
    java.lang.IllegalArgumentException - if names is not a valid column name array of names as determined by checkNames.
  - TableColumnCollection
```
public TableColumnCollection(java.lang.Object... names)
```
    Creates a new table-column names collection.
    The new instance will have its own copy of the input name array, thus is safe to modify such an array after calling this constructor; it won't modify the state of this object.
    
    Parameters:
    
    names - the column names. They will be transformed into strings using toString.
    
    Throws:
    
    java.lang.IllegalArgumentException - if names is not a valid column name array of names as determined by checkNames.
  - TableColumnCollection
```
public TableColumnCollection(java.lang.Class<? extends java.lang.Enum<?>> enumClass)
```
    Creates a new table-column collection from a set of enum constants.
    The new instance will have one column for enum value in enumClass, in their ordinal order.
    
    The toString transformation of each constant is used as the column name. Notice that this might differ from the constant name if this method is overloaded by the enum.
    
    Parameters:
    
    enumClass - the input enum class.
    
    Throws:
    
    java.lang.IllegalArgumentException - if enumClass is null or is actually not an enum class or the corresponding names are illegal.
- Method Detail
  - names
```
public java.util.List<java.lang.String> names()
```
    Returns the column names ordered by column index.
    
    Returns:
    
    never null, a unmodifiable view to this collection column names.
  - nameAt
```
public java.lang.String nameAt(int index)
```
    Returns the name of a column by its index.
    Column indexes are 0-based.
    
    Parameters:
    
    index - the target column index.
    
    Returns:
    
    never null.
    
    Throws:
    
    java.lang.IllegalArgumentException - if index is not a valid column index.
  - indexOf
```
public int indexOf(java.lang.String name)
```
    Returns the index of a column by its name.
    
    Parameters:
    
    name - the query column name.
    
    Returns:
    
    -1 if there is not such a column, 0 or greater otherwise.
  - contains
```
public boolean contains(java.lang.String name)
```
    Check whether there is such a column by name.
    
    Parameters:
    
    name - the query name.
    
    Returns:
    
    true iff there is a column with such a name.
    
    Throws:
    
    java.lang.IllegalArgumentException - if name is null.
  - containsAll
```
public boolean containsAll(java.lang.String... names)
```
    Checks whether columns contain all the names in an array.
    
    Parameters:
    
    names - the names to test.
    
    Returns:
    
    true iff all the names in names correspond to columns in this collection.
    
    Throws:
    
    java.lang.IllegalArgumentException - if names is null or contains any null.
  - containsAll
```
public boolean containsAll(java.lang.Iterable<java.lang.String> names)
```
    Checks whether columns contain all the names in an array.
    
    Parameters:
    
    names - the names to test.
    
    Returns:
    
    true iff all the names in names correspond to columns in this collection.
    
    Throws:
    
    java.lang.IllegalArgumentException - if names is null or contains any null.
  - containsExactly
```
public boolean containsExactly(java.lang.String... names)
```
    Checks whether columns contain all the names in an array and no other.
    
    Parameters:
    
    names - the names to test.
    
    Returns:
    
    true iff all the names in names correspond to columns in this collection, and there is no other column name.
    
    Throws:
    
    java.lang.IllegalArgumentException - if names is null or contains null.
  - matches
```
public boolean matches(int index,
                       java.lang.String name)
```
    Checks a column names matches given one.
    A match against a column index beyond the last column returns false.
    
    Parameters:
    
    index - the column index to test.
    
    name - the expected column name.
    
    Returns:
    
    true iff the the column at index's name is equal to the input name.
    
    Throws:
    
    java.lang.IllegalArgumentException - if name is null or index is negative.
  - matchesAll
```
public boolean matchesAll(int offset,
                          java.lang.String... names)
```
    Checks an array of column matches the column names starting from a given index.
    
    Parameters:
    
    offset - the column index to match to the first name in names test.
    
    names - the expected column names.
    
    Returns:
    
    true iff the the column names starting from index is equal to the input names.
    
    Throws:
    
    java.lang.IllegalArgumentException - if names is null, contains any null or index is not a valid index.
  - matchesExactly
```
public boolean matchesExactly(java.lang.String... names)
```
    Checks whether columns contain all the names in an array and no other and in the very same order.
    
    Parameters:
    
    names - the names to test.
    
    Returns:
    
    true iff all the names in names correspond to columns in this collection in the same order, and there is no other column.
    
    Throws:
    
    java.lang.IllegalArgumentException - if names is null or contains null.
  - columnCount
```
public int columnCount()
```
    Returns the number of columns.
    
    Returns:
    
    never column
  - checkNames
```
public static java.lang.String[] checkNames(java.lang.Object[] columnNames,
                                            java.util.function.Function<java.lang.String,java.lang.RuntimeException> exceptionFactory)
```
    Checks that a column name, as objects, array is valid.
    The actual column names to test are obtained by mapping its object to its string representation using toString.
    
    Assuming that it is null-value free, a column name array is invalid if:
    - has length 0,
    - the first name contains the comment prefix,
    - or contains repeats
    When the input array is invalid, an exception is thrown using the exception factory function provided.
    
    The message passed to the factory explains why the column name array is invalid
    .
    Notice that a null array or a null containing array is considered a illegal argument caused by a bug and a IllegalArgumentException will be thrown instead.
    Returns:
    
    never null, the same reference as the input column name array columnNames.
    
    Throws:
    
    java.lang.IllegalArgumentException - if columnNames is null, or it contains any null, or exceptionFactory is null or ir returns a null when invoked.
    
    java.lang.RuntimeException - if columnNames does not contain a valid list of column names. The exact type will depend on the input exceptionFactory.
  - checkNames
```
public static java.lang.String[] checkNames(java.lang.String[] columnNames,
                                            java.util.function.Function<java.lang.String,java.lang.RuntimeException> exceptionFactory)
```
    Checks that a column name array is valid.
    Assuming that it is null-value free, a column name array is invalid if:
    - has length 0,
    - the first name contains the comment prefix,
    - or contains repeats
    When the input array is invalid, an exception is thrown using the exception factory function provided.
    
    The message passed to the factory explains why the column name array is invalid
    .
    Notice that a null array or a null containing array is considered a illegal argument caused by a bug an a IllegalArgumentException will be thrown instead.
    Returns:
    
    never null, the same reference as the input column name array columnNames.
    
    Throws:
    
    java.lang.IllegalArgumentException - if columnNames is null, or it contains any null, or exceptionFactory is null or ir returns a null when invoked.
    
    java.lang.RuntimeException - if columnNames does not contain a valid list of column names. The exact type will depend on the input exceptionFactory.
  - equals
```
public boolean equals(java.lang.Object o)
```
    Overrides:
    
    equals in class java.lang.Object
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class java.lang.Object

Class TableColumnCollection

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

TableColumnCollection

TableColumnCollection

TableColumnCollection

TableColumnCollection

Method Detail

names

nameAt

indexOf

contains

containsAll

containsAll

containsExactly

matches

matchesAll

matchesExactly

columnCount

checkNames

checkNames

equals

hashCode