protected class ProteinTree.SequenceIndexer
extends java.lang.Object
implements java.lang.Runnable
Modifier and Type | Field and Description |
---|---|
protected boolean |
addToTree
Boolean indicating whether the accession should be considered or not
|
protected boolean |
displayProgress
Boolean indicating whether progress should be displayed.
|
protected Enzyme |
enzyme
The enzyme to use.
|
protected boolean |
finished
Boolean indicating whether the thread shall be interrupted.
|
protected java.util.HashMap<java.lang.String,java.util.ArrayList<java.lang.Integer>> |
indexes
The result of the indexing.
|
protected int |
initialTagSize
Integer indicating the initial length of considered peptides, also
indicates the depth of a node
|
protected java.util.concurrent.BlockingQueue<Protein> |
proteinQueue
The protein sequence to index.
|
protected java.util.ArrayList<java.lang.String> |
tags
List of tags to inspect.
|
protected WaitingHandler |
waitingHandler
The waiting handler.
|
Constructor and Description |
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ProteinTree.SequenceIndexer(java.util.concurrent.BlockingQueue<Protein> proteinQueue,
java.util.ArrayList<java.lang.String> tags,
int initialTagSize,
Enzyme enzyme,
WaitingHandler waitingHandler,
boolean displayProgress)
Constructor.
|
Modifier and Type | Method and Description |
---|---|
java.util.HashMap<java.lang.String,java.util.ArrayList<java.lang.Integer>> |
getIndexes()
Returns the indexes.
|
protected java.util.HashMap<java.lang.String,java.util.ArrayList<java.lang.Integer>> |
getTagToIndexesMap(java.lang.String sequence,
java.util.ArrayList<java.lang.String> tags,
Enzyme enzyme)
Returns all the positions of the given tags on the given sequence in
a map: tag -> list of indexes in the sequence.
|
boolean |
isFinished()
Indicates whether the run is finished.
|
void |
run() |
protected java.util.concurrent.BlockingQueue<Protein> proteinQueue
protected boolean finished
protected java.util.ArrayList<java.lang.String> tags
protected Enzyme enzyme
protected java.util.HashMap<java.lang.String,java.util.ArrayList<java.lang.Integer>> indexes
protected WaitingHandler waitingHandler
protected boolean displayProgress
protected boolean addToTree
protected int initialTagSize
public ProteinTree.SequenceIndexer(java.util.concurrent.BlockingQueue<Protein> proteinQueue, java.util.ArrayList<java.lang.String> tags, int initialTagSize, Enzyme enzyme, WaitingHandler waitingHandler, boolean displayProgress)
proteinSequence
- the protein sequencetags
- the tags to inspectenzyme
- the enzyme to use, can be nullpublic void run()
run
in interface java.lang.Runnable
public boolean isFinished()
public java.util.HashMap<java.lang.String,java.util.ArrayList<java.lang.Integer>> getIndexes()
protected java.util.HashMap<java.lang.String,java.util.ArrayList<java.lang.Integer>> getTagToIndexesMap(java.lang.String sequence, java.util.ArrayList<java.lang.String> tags, Enzyme enzyme) throws java.sql.SQLException, java.io.IOException, java.lang.ClassNotFoundException
sequence
- the sequence of interesttags
- the tags of interestenzyme
- the enzyme restrictionjava.sql.SQLException
java.io.IOException
java.lang.ClassNotFoundException
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