de.unibi.techfak.jpredictor.motifs
Class MotifSearchAdapter.SearchFields

java.lang.Object
  de.unibi.techfak.jpredictor.motifs.MotifSearchAdapter.SearchFields

Enclosing class:

MotifSearchAdapter

protected class MotifSearchAdapter.SearchFields
extends java.lang.Object

Holds data structures and fields relevant for searching motifs.

Field Summary

protected int[][]	matchMatrixMinus The two matrices where all match results of the motif with every possible char are stored.
protected int[][]	matchMatrixPlus The two matrices where all match results of the motif with every possible char are stored.
protected double[]	probArrayMinus The two arrays where the probabilities of occurrences of motif characters are stored.
protected double[]	probArrayPlus The two arrays where the probabilities of occurrences of motif characters are stored.
private int	searchMode The mode to search for the motif.
protected java.util.LinkedList	searchResults Its a list that holds the occurrences of the found motif on the searchSequence, set by the method search from the Interface MotifSearcher
protected java.lang.CharSequence	searchSequence Its the sequence where the motif is to search in.
protected int	sequenceWindowStart The search start on the sequence, set by initSearchWindow.
protected int	sequenceWindowWidth The width of the window on the sequence to search, set by initSearchWindow.

Constructor Summary

protected

MotifSearchAdapter.SearchFields()

Method Summary

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

searchSequence

protected java.lang.CharSequence searchSequence

Its the sequence where the motif is to search in. It is set by 'initSearch' and used by 'search', both from the Interface 'MotifSearcher'.

See Also:

MotifSearcher.initSearch(CharSequence), MotifSearcher.search(int, int)

searchResults

protected java.util.LinkedList searchResults

Its a list that holds the occurrences of the found motif on the searchSequence, set by the method search from the Interface MotifSearcher

See Also:

MotifSearcher.initSearch(CharSequence), MotifSearcher.search(int, int)

sequenceWindowStart

protected int sequenceWindowStart

The search start on the sequence, set by initSearchWindow. Default is 0.

See Also:

MotifSearcher.search(int, int)

sequenceWindowWidth

protected int sequenceWindowWidth

The width of the window on the sequence to search, set by initSearchWindow. Default is Integer.MAX_VALUE.

See Also:

MotifSearcher.search(int, int)

searchMode

private int searchMode

The mode to search for the motif. Valid are: SEARCH_DIRECTION_PLUS, SEARCH_DIRECTION_MINUS and SEARCH_ALL_ORIENTATIONS.

See Also:

MotifSearcher.setSearchMode(int), MotifSearcher.getSearchMode(), MotifSearcher.SEARCH_DIRECTION_PLUS, MotifSearcher.SEARCH_DIRECTION_MINUS, MotifSearcher.SEARCH_ALL_ORIENTATIONS

matchMatrixPlus

protected int[][] matchMatrixPlus

The two matrices where all match results of the motif with every possible char are stored. This is for fast access, thus the match-methods have to be called only while initialization.
It is stored a zero, if we have a match and a one if we have a mismatch.
One matrix is for plus search direction and one is for minus (reversed complemented) search orientation.

matchMatrixMinus

protected int[][] matchMatrixMinus

The two matrices where all match results of the motif with every possible char are stored. This is for fast access, thus the match-methods have to be called only while initialization.
It is stored a zero, if we have a match and a one if we have a mismatch.
One matrix is for plus search direction and one is for minus (reversed complemented) search orientation.

probArrayPlus

protected double[] probArrayPlus

The two arrays where the probabilities of occurrences of motif characters are stored. This is for fast access, thus the match-methods have to be called only while initialization.
One matrix is for plus search direction and one is for minus (reversed complementary) search orientation.

probArrayMinus

protected double[] probArrayMinus

The two arrays where the probabilities of occurrences of motif characters are stored. This is for fast access, thus the match-methods have to be called only while initialization.
One matrix is for plus search direction and one is for minus (reversed complementary) search orientation.

Constructor Detail

MotifSearchAdapter.SearchFields

protected MotifSearchAdapter.SearchFields()