SamReader.AssertingIterator (htsjdk 2.14.3 API)

java.lang.Object
- htsjdk.samtools.SamReader.AssertingIterator

All Implemented Interfaces:

SAMRecordIterator, CloseableIterator<SAMRecord>, Closeable, AutoCloseable, Iterator<SAMRecord>

Enclosing interface:

SamReader
```
public static class SamReader.AssertingIterator
extends Object
implements SAMRecordIterator
```

Constructor Summary

Constructors
Constructor Description

AssertingIterator(CloseableIterator<SAMRecord> iterator)

Constructors
Constructor	Description
`AssertingIterator(CloseableIterator<SAMRecord> iterator)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`SAMRecordIterator`	`assertSorted(SAMFileHeader.SortOrder sortOrder)`	Establishes that records returned by this iterator are expected to be in the specified sort order.
`void`	`close()`	Should be implemented to close/release any underlying resources.
`boolean`	`hasNext()`
`SAMRecord`	`next()`
`void`	`remove()`

Methods inherited from interface htsjdk.samtools.util.CloseableIterator
stream, toList

Methods inherited from interface java.util.Iterator
forEachRemaining

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

- Constructor Detail
  - AssertingIterator
```
public AssertingIterator(CloseableIterator<SAMRecord> iterator)
```
- Method Detail
  - assertSorted
```
public SAMRecordIterator assertSorted(SAMFileHeader.SortOrder sortOrder)
```
    Description copied from interface: SAMRecordIterator
    
    Establishes that records returned by this iterator are expected to be in the specified sort order. If this method has been called, then implementers must throw an IllegalStateException from next() when a record is read that violates the sort order. This method may be called multiple times over the course of an iteration, changing the expected sort, if desired -- from the time it is called, it validates whatever sort is set, or stops validating if it is set to null or SAMFileHeader.SortOrder.unsorted. If this method is not called, then no validation of the iterated records is done.
    
    Specified by:
    
    assertSorted in interface SAMRecordIterator
    
    Parameters:
    
    sortOrder - The order in which records are expected to be returned
    
    Returns:
    
    This SAMRecordIterator
  - next
```
public SAMRecord next()
```
    Specified by:
    
    next in interface Iterator<SAMRecord>
  - close
```
public void close()
```
    Description copied from interface: CloseableIterator
    
    Should be implemented to close/release any underlying resources.
    
    Specified by:
    
    close in interface AutoCloseable
    
    Specified by:
    
    close in interface Closeable
    
    Specified by:
    
    close in interface CloseableIterator<SAMRecord>
  - hasNext
```
public boolean hasNext()
```
    Specified by:
    
    hasNext in interface Iterator<SAMRecord>
  - remove
```
public void remove()
```
    Specified by:
    
    remove in interface Iterator<SAMRecord>

Class SamReader.AssertingIterator

Constructor Summary

Method Summary

Methods inherited from interface htsjdk.samtools.util.CloseableIterator

Methods inherited from interface java.util.Iterator

Methods inherited from class java.lang.Object

Constructor Detail

AssertingIterator

Method Detail

assertSorted

next

close

hasNext

remove