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package stream;
import structures.ListNum;
public interface ConcurrentReadStreamInterface extends Runnable{
/** Start this in a new thread. */
public void start();
/** Fetch the next list of reads. Returns an empty list when end of input is reached. */
public ListNum<Read> nextList();
/** Re-calls returnList(returnList(ln.id, ln.list.isEmpty()) */
public void returnList(ListNum<Read> ln);
/** When the nextList() caller is done processing a list, it MUST be returned using this method.
* The 'poison' flag should be set to false normally. When a consumer thread receives an empty list from nextList(),
* it should be returned with the poison flag set to true, then the consumer should terminate.
* This will return a list to the 'full' queue, allowing another thread to pull the empty list and terminate. */
public void returnList(long listNumber, boolean poison);
/** This must be called (indirectly, via Thread.start()) before reads will be generated. */
@Override
public void run();
/** Indicate to producer threads that no more reads are desired, and interrupts them. */
public void shutdown();
/** Reset state to allow production of reads from the beginning of the input files.
* Does not work with stdin (may cause strange behavior). */
public void restart();
/** Calls shutdown, then shuts down all threads and closes all associated files. */
public void close();
/** Returns true for paired-end stream, false for single-end stream. */
public boolean paired();
/** Name of the file or resource underlying this stream */
public String fname();
/** Returns the underlying read object producer(s), such as ReadInputStreams. Optional method for things such as error messages. */
public Object[] producers();
/** Return true if this stream or its producers have detected an error. */
public boolean errorState();
/**
* Set the read sampling rate. Optional method.
* @param rate Fraction of reads to use, 0-1.
* @param seed Random number generator seed when positive. If negative, a random seed will be used.
*/
public void setSampleRate(float rate, long seed);
/**
* @return Number of bases read by this stream.
*/
public long basesIn();
/**
* @return Number of reads read by this stream.
*/
public long readsIn();
/**
* @return Value of verbose field.
*/
public boolean verbose();
// public String classname(); //e.g. getClass().getName()
}
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