modele
Class OriginAlgoStefanConverter

java.lang.Object
  modele.OriginAlgoStefanConverter

public abstract class OriginAlgoStefanConverter
extends java.lang.Object

Linked with class OriginAlgorithmsStefan OriginAlgorithmsStefan to avoid to be too long : some conversion procedures are here as sttatic statements.
Mainly work as an helper for that things.

Since:

August 29, 2008

Author:

Gabriel Chandesris (2008)

Constructor Summary

OriginAlgoStefanConverter()

Method Summary

private static java.lang.String	afficher_Caracteristique_Web(ADN1cible target, OriginAlgorithmsStefan algo, boolean tfold) Some changes to this procedure to make results appears for web / HTML.
private static java.lang.String	afficher_Caracteristique(ADN1cible target, OriginAlgorithmsStefan algo, boolean tfold) SOME SHOW FOR VIEW "This method for show on a target sequence of DNA"
private static java.lang.String	afficherNom_web(ADN1test[] tabAdn) Some changes to this procedure to make results appears for web / HTML.
private static java.lang.String	afficherNom(ADN1test[] tabAdn) To bet the name of a tab of instances of ADN1test.
static SequenceListe	algoSSCA(Sequence target, SequenceListe homologuous) Deprecated. "old version" see also algoSSCA(Sequence, SequenceListe, int, int)
static SequenceListe	algoSSCA(Sequence target, SequenceListe homologuous, int identity, int deletion) A default call to SSCA algorithm to get all list of homologuous with scores computed.
static SequenceListe	algoSSCA(Sequence target, SequenceListe homologuous, int nbMinSequences, int nbMaxSequences, double minHomology, double maxHomology, boolean selection) Deprecated. "old version" see also algoSSCA(Sequence, SequenceListe, int, int, double, double, boolean, int, int)
static SequenceListe	algoSSCA(Sequence target, SequenceListe homologuous, int nbMinSequences, int nbMaxSequences, double minHomology, double maxHomology, boolean selection, int identity, int deletion) The whole computing of SSCA.
static void	computingStatic(java.util.Vector tabsadn, ADN1cible adncible, boolean morePrediction, boolean searchPseudoknots) Deprecated. [old test version]
static java.util.Vector	conversionFrom(ADN1test adntcible, SequenceListe[] listes) Conversion of a set of sequences listes to a vector of tabs of ADN1test's and put the target sequence at position 0 on each table.
static ADN1test[]	conversionFrom(SequenceListe liste) Conversion of a set of sequences listes to a tab of ADN1test's.
static java.util.Vector	conversionFrom(SequenceListe[] listes) Conversion of a set of sequences listes to a vector of tabs of ADN1test's Do not forget that target sequence must be on position 0 of each table !
static Palindrome1cible	convertFrom(Palindrome pal) To get a "target palindrome" from Palindrome.
static ADN1cible	convertFrom(Sequence cible) To get a "cible sequence" from an instance of Sequence.
static ADN1test	convertFrom(Sequence cible, int diff) To get a "test sequence" from an instance of Sequence.
private static java.lang.String	decoupeString_Web(java.lang.String chaineDecoupe) This method to cut a String by 80 characters length substring.
private static java.lang.String	decoupeString(java.lang.String chaineDecoupe) This method to cut a String by 80 characters length substring.
private static ADN1test[]	distance(ADN1cible adn, ADN1test adncible, ADN1test[] adntest) Deprecated. "old version" see also distance(ADN1cible, ADN1test, ADN1test[], int, int)
private static ADN1test[]	distance(ADN1cible adn, ADN1test adncible, ADN1test[] adntest, int identity, int deletion) "procedure which give a score to the test sequence and sort them. " First part of SSCA algorithm : scores !
static Palindrome1cible[]	fusion_Palindrome(Palindrome1cible[] tabPalCourant, Palindrome1cible[] tabPalPrincipal) "Following methods sorted by use order in ADN1 Class". (6) "Fusion method of two tables of palindromes to have the final table of result step by step ; used by palindromes' search"
static java.lang.String	getScreenToSee(java.util.Vector tabsadn, ADN1cible target, OriginAlgorithmsStefan algo, boolean tfold) Working about what will be on screen.
static java.lang.String	getScreenToSeeHTML(java.util.Vector tabsadn, ADN1cible target, OriginAlgorithmsStefan algo, boolean tfold) Working about what will be on screen.
private static ADN1test[]	trier(ADN1test adncible, ADN1test[] adntest, int quelscore) To sort the tab...

Methods inherited from class java.lang.Object

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

Constructor Detail

OriginAlgoStefanConverter

public OriginAlgoStefanConverter()

Method Detail

conversionFrom

public static java.util.Vector conversionFrom(SequenceListe[] listes)

Conversion of a set of sequences listes to a vector of tabs of ADN1test's
Do not forget that target sequence must be on position 0 of each table !
Conversion and settings.

Parameters:

listes - (SequenceListe[])

Returns:

(Vector) Vector of tabs of ADN1tests

See Also:

ADN1test, Sequence, SequenceListe, controller

conversionFrom

public static java.util.Vector conversionFrom(ADN1test adntcible,
                                              SequenceListe[] listes)

Conversion of a set of sequences listes to a vector of tabs of ADN1test's
and put the target sequence at position 0 on each table.
Conversion and settings.

Parameters:

listes - (SequenceListe[])

Returns:

(Vector) Vector of tabs of ADN1tests

See Also:

ADN1test, Sequence, SequenceListe, controller

conversionFrom

public static ADN1test[] conversionFrom(SequenceListe liste)

Conversion of a set of sequences listes to a tab of ADN1test's.
Conversion and settings.

Parameters:

liste - (SequenceListe)

Returns:

(ADN1test[]) Tab of ADN1tests

See Also:

ADN1test, Sequence, SequenceListe

convertFrom

public static ADN1cible convertFrom(Sequence cible)

To get a "cible sequence" from an instance of Sequence.
Conversion and settings.

Parameters:

cible - (Sequence)

Returns:

(ADN1cible)

See Also:

ADN1cible, Sequence

convertFrom

public static ADN1test convertFrom(Sequence cible,
                                   int diff)

To get a "test sequence" from an instance of Sequence.
Conversion and settings.

Parameters:

cible - (Sequence)

diff - (int) [unused] 42 is a good use

Returns:

(ADN1test)

See Also:

ADN1test, Sequence

convertFrom

public static Palindrome1cible convertFrom(Palindrome pal)

To get a "target palindrome" from Palindrome.

Parameters:

pal - (Palindrome)

Returns:

(Palindrome1cible)

getScreenToSee

public static java.lang.String getScreenToSee(java.util.Vector tabsadn,
                                              ADN1cible target,
                                              OriginAlgorithmsStefan algo,
                                              boolean tfold)

Working about what will be on screen.
Conversion and settings.

Parameters:

tabsadn - (Vector) vector of tabs of palindromes

target - (ADN1cible)

tfold - (boolean) false if multiple predictions (TFold), true if one (P-DCFold)

Returns:

(String)

See Also:

afficherNom(ADN1test[]), Interface3.visualize(PalindromeListe)

afficherNom

private static java.lang.String afficherNom(ADN1test[] tabAdn)

To bet the name of a tab of instances of ADN1test.
Indication about black box : first sequence excluded from show : target sequence ?
Conversion and settings.

Parameters:

tabAdn - (ADN1test[])

Returns:

(String)

See Also:

getScreenToSee(Vector, ADN1cible, OriginAlgorithmsStefan, boolean), getScreenToSeeHTML(Vector, ADN1cible, OriginAlgorithmsStefan, boolean)

afficher_Caracteristique

private static java.lang.String afficher_Caracteristique(ADN1cible target,
                                                         OriginAlgorithmsStefan algo,
                                                         boolean tfold)

SOME SHOW FOR VIEW
"This method for show on a target sequence of DNA"

Parameters:

target - (ADN1cible) target sequence

algo - (OriginAlgorithmsStefan)

tfold - (boolean) false if multiple predictions (TFold), true if one (P-DCFold)

Returns:

(String)

See Also:

Interface3.setInterface(ADN1cible, Vector)

decoupeString

private static java.lang.String decoupeString(java.lang.String chaineDecoupe)

This method to cut a String by 80 characters length substring.

Parameters:

chaineDecoupe - (String)

Returns:

(String)

Since:

August 2008

See Also:

ProcessusOrigin.doPost(HttpServletRequest, HttpServletResponse)

getScreenToSeeHTML

public static java.lang.String getScreenToSeeHTML(java.util.Vector tabsadn,
                                                  ADN1cible target,
                                                  OriginAlgorithmsStefan algo,
                                                  boolean tfold)

Working about what will be on screen.
Conversion and settings.

Parameters:

tabsadn - (Vector) vector of tabs of palindromes

target - (ADN1cible)

algo - (OriginAlgorithmsStefan)

tfold - (boolean) false if multiple predictions (TFold), true if one (P-DCFold)

Returns:

(String) HTML format vizualization...

See Also:

afficherNom_web(ADN1test[])

afficherNom_web

private static java.lang.String afficherNom_web(ADN1test[] tabAdn)

Some changes to this procedure to make results appears for web / HTML.
Conversion and settings.

Parameters:

tabAdn - (ADN1test[])

Returns:

(String)

See Also:

getScreenToSee(Vector, ADN1cible, OriginAlgorithmsStefan, boolean), getScreenToSeeHTML(Vector, ADN1cible, OriginAlgorithmsStefan, boolean)

afficher_Caracteristique_Web

private static java.lang.String afficher_Caracteristique_Web(ADN1cible target,
                                                             OriginAlgorithmsStefan algo,
                                                             boolean tfold)

Some changes to this procedure to make results appears for web / HTML.

Parameters:

target - (ADN1cible) target sequence

algo - (OriginAlgorithmsStefan)

tfold - (boolean) false if multiple predictions (TFold), true if one (P-DCFold)

Returns:

(String) HTML view.

Since:

August 2008

decoupeString_Web

private static java.lang.String decoupeString_Web(java.lang.String chaineDecoupe)

This method to cut a String by 80 characters length substring.

Parameters:

chaineDecoupe - (String)

Returns:

(String)

Since:

August 2008

computingStatic

public static void computingStatic(java.util.Vector tabsadn,
                                   ADN1cible adncible,
                                   boolean morePrediction,
                                   boolean searchPseudoknots)

Deprecated. [old test version]

Computing the main algorithm made by Stefan Engelen.
Result is structures contained by adncible.
Not static because of need of some parameters in Processsus.
Conversion and settings.

Parameters:

tabsadn - (Vector) Vector of tabs of ADN1tests, target at position 0 !

adncible - (ADN1test) target sequence

morePrediction - (boolean) if more than one structure as result or not

searchPseudoknots - (boolean) Searching pseudoknots or not

See Also:

conversionFrom(SequenceListe[]), OriginAlgorithmsStefan.getRecordingStructures(ADN1cible), getScreenToSee(Vector, ADN1cible, OriginAlgorithmsStefan, boolean), getScreenToSeeHTML(Vector, ADN1cible, OriginAlgorithmsStefan, boolean)

fusion_Palindrome

public static Palindrome1cible[] fusion_Palindrome(Palindrome1cible[] tabPalCourant,
                                                   Palindrome1cible[] tabPalPrincipal)

"Following methods sorted by use order in ADN1 Class". (6)
"Fusion method of two tables of palindromes to have the final table of result step by step ; used by palindromes' search"

Parameters:

tabPalCourant - (Palindrome1cible[])

tabPalPrincipal - (Palindrome1cible[])

Returns:

(Palindrome1cible[])

See Also:

ArbrePalindrome.recuperation(Vector, Palindrome1cible[], NoeudPalindrome), OriginAlgorithmsStefan.recherche_Palindrome(ADN1cible, int, int, int, ADN1test[], int, int, boolean, int)

algoSSCA

public static SequenceListe algoSSCA(Sequence target,
                                     SequenceListe homologuous)

Deprecated. "old version" see also algoSSCA(Sequence, SequenceListe, int, int)

A default call to SSCA algorithm to get all list of homologuous with scores computed.

Parameters:

target - (Sequence) target sequences

homologuous - (SequenceListe) homologuous sequences

Returns:

(SequenceListe)

See Also:

algoSSCA(Sequence, SequenceListe, int, int, double, double, boolean)

algoSSCA

public static SequenceListe algoSSCA(Sequence target,
                                     SequenceListe homologuous,
                                     int nbMinSequences,
                                     int nbMaxSequences,
                                     double minHomology,
                                     double maxHomology,
                                     boolean selection)

Deprecated. "old version" see also algoSSCA(Sequence, SequenceListe, int, int, double, double, boolean, int, int)

The whole computing of SSCA.
Selection of scores with criteria is as follow :

1. Selection with homology is applied
2. If not enough : selection as minimal / maximal for first sorted sequences

Parameters:

target - (Sequence) target sequence

homologuous - (SequenceListe) homologuous sequences

nbMinSequences - (int) minimal number of sequences to be selected

nbMaxSequences - (int) maximal number of sequences to be selected

minHomology - (double) minimal homology for selection

maxHomology - (double) maximal homology for selection

selection - (boolean) To output the selection (true) or all sequences (false)

Returns:

(SequenceListe)

distance

private static ADN1test[] distance(ADN1cible adn,
                                   ADN1test adncible,
                                   ADN1test[] adntest)

Deprecated. "old version" see also distance(ADN1cible, ADN1test, ADN1test[], int, int)

"procedure which give a score to the test sequence and sort them. "
First part of SSCA algorithm : scores !

Parameters:

adn - (ADN1cible) target sequence

adncible - (ADN1test) target sequence

adntest - (ADN1test[]) same as return ?

Returns:

(ADN1test[]) same as argument (modulo the scores and sort) ?

See Also:

Profil, trier(ADN1test, ADN1test[], int)

algoSSCA

public static SequenceListe algoSSCA(Sequence target,
                                     SequenceListe homologuous,
                                     int identity,
                                     int deletion)

A default call to SSCA algorithm to get all list of homologuous with scores computed.

Parameters:

target - (Sequence) target sequences

homologuous - (SequenceListe) homologuous sequences

identity - (int) best percentage of identity

deletion - (int) percentage of deletion

Returns:

(SequenceListe)

See Also:

algoSSCA(Sequence, SequenceListe, int, int, double, double, boolean, int, int)

algoSSCA

public static SequenceListe algoSSCA(Sequence target,
                                     SequenceListe homologuous,
                                     int nbMinSequences,
                                     int nbMaxSequences,
                                     double minHomology,
                                     double maxHomology,
                                     boolean selection,
                                     int identity,
                                     int deletion)

The whole computing of SSCA.
Selection of scores with criteria is as follow :

1. Selection with homology is applied
2. If not enough : selection as minimal / maximal for first sorted sequences

Parameters:

target - (Sequence) target sequence

homologuous - (SequenceListe) homologuous sequences

nbMinSequences - (int) minimal number of sequences to be selected

nbMaxSequences - (int) maximal number of sequences to be selected

minHomology - (double) minimal homology for selection

maxHomology - (double) maximal homology for selection

identity - (int) best percentage of identity

deletion - (int) percentage of deletion

selection - (boolean) To output the selection (true) or all sequences (false)

Returns:

(SequenceListe)

distance

private static ADN1test[] distance(ADN1cible adn,
                                   ADN1test adncible,
                                   ADN1test[] adntest,
                                   int identity,
                                   int deletion)

"procedure which give a score to the test sequence and sort them. "
First part of SSCA algorithm : scores !

Parameters:

adn - (ADN1cible) target sequence

adncible - (ADN1test) target sequence

adntest - (ADN1test[]) same as return ?

identity - (int) best percentage of identity

deletion - (int) percentage of deletion

Returns:

(ADN1test[]) same as argument (modulo the scores and sort) ?

See Also:

Profil, trier(ADN1test, ADN1test[], int)

trier

private static ADN1test[] trier(ADN1test adncible,
                                ADN1test[] adntest,
                                int quelscore)

To sort the tab...

Parameters:

adncible - (ADN1test)

adntest - (ADN1test[])

quelscore - (int)

Returns:

(ADN1test[])

See Also:

ADN1test.distance(ADN1cible, ADN1test, ADN1test[])