| Modifier and Type | Class and Description |
|---|---|
class |
Clustering<T,S extends Sequence<S>> |
| Modifier and Type | Class and Description |
|---|---|
class |
AbstractMultiReader<R extends SequenceRead>
Created by dbolotin on 23/06/14.
|
class |
MultiReader |
class |
PairedReader
Created by dbolotin on 23/06/14.
|
| Modifier and Type | Class and Description |
|---|---|
class |
FastaReader<S extends Sequence<S>>
Reads amino acid or nucleotide sequence from FASTA formatted file
|
class |
FastaSequenceReaderWrapper
|
| Modifier and Type | Class and Description |
|---|---|
class |
PairedFastqReader
Created by dbolotin on 23/06/14.
|
class |
SingleFastqIndexer |
class |
SingleFastqReader |
| Modifier and Type | Class and Description |
|---|---|
class |
PipeReader<O> |
class |
PReader |
| Modifier and Type | Interface and Description |
|---|---|
interface |
CanReportProgressAndStage |
| Modifier and Type | Class and Description |
|---|---|
class |
ProgressAndStage |
| Modifier and Type | Method and Description |
|---|---|
static CanReportProgress |
SmartProgressReporter.extractProgress(cc.redberry.pipe.util.CountingOutputPort<?> countingOutputPort,
long size) |
static CanReportProgress |
SmartProgressReporter.extractProgress(cc.redberry.pipe.util.CountLimitingOutputPort<?> countLimitingOutputPort) |
CanReportProgress |
CountingInputStream.getProgressReporter(long totalSize) |
| Modifier and Type | Method and Description |
|---|---|
static void |
SmartProgressReporter.startProgressReport(String prefix,
CanReportProgress reporter) |
static void |
SmartProgressReporter.startProgressReport(String prefix,
CanReportProgress reporter,
PrintStream stream) |
| Constructor and Description |
|---|
SmartProgressReporter(String prefix,
CanReportProgress reporter) |
SmartProgressReporter(String prefix,
CanReportProgress reporter,
PrintStream stream) |
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