modele
Class AlgoStefanConverter

java.lang.Object
  modele.AlgoStefanConverter

public abstract class AlgoStefanConverter
extends java.lang.Object

Linked with class AlgorithmsStefan AlgorithmsStefan to avoid to be too long : some conversion procedures are here as sttatic statements.
Mainly work as an helper for that things.
Vector's have been removed, import of ADN1test has been kept. For more information see AlgorithmsStefan.

Since:

August 29, 2008, September 3, 2008

Version:

September 4, 2008

Author:

Gabriel Chandesris (2008)

Constructor Summary

AlgoStefanConverter()

Method Summary

private static java.lang.String	afficher_Caracteristique_Web(Sequence target, AlgorithmsStefan algo, boolean tfold) Some changes to this procedure to make results appears for web / HTML.
private static java.lang.String	afficher_Caracteristique(Sequence target, AlgorithmsStefan algo, boolean tfold) SOME SHOW FOR VIEW "This method for show on a target sequence of DNA"
private static java.lang.String	afficherNom_web(Sequence[] tabAdn) Some changes to this procedure to make results appears for web / HTML.
private static java.lang.String	afficherNom(Sequence[] tabAdn) To bet the name of a tab of instances of Sequence.
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 java.util.Vector	conversionFrom(Sequence adntcible, SequenceListe[] listes) Deprecated. [only for information, please use conversionFrom(Sequence, SequenceListe[], boolean)]
static SequenceListe[]	conversionFrom(Sequence adntcible, SequenceListe[] listes, boolean diff) 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.
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 Sequence[]	distance(Sequence target_cible, Sequence target_test, Sequence[] adntest) Deprecated. "old version" see also distance(Sequence, Sequence, Sequence[], int, int)
private static Sequence[]	distance(Sequence target_cible, Sequence target_test, Sequence[] adntest, int identity, int deletion) "procedure which give a score to the test sequence and sort them. " First part of SSCA algorithm : scores !
static Palindrome[]	fusion_Palindrome(Palindrome[] tabPalCourant, Palindrome[] 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(SequenceListe[] tabsadn, Sequence target, AlgorithmsStefan algo, boolean tfold) Working about what will be on screen.
static java.lang.String	getScreenToSeeHTML(SequenceListe[] tabsadn, Sequence target, AlgorithmsStefan algo, boolean tfold) Working about what will be on screen.
private static Sequence[]	trier(Sequence target_test, Sequence[] 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

AlgoStefanConverter

public AlgoStefanConverter()

Method Detail

conversionFrom

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

Deprecated. [only for information, please use conversionFrom(Sequence, SequenceListe[], boolean)]

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:

adntcible - (Sequence) target sequence to add in position 0

listes - (SequenceListe[])

Returns:

(Vector) Vector of tabs of Sequences

See Also:

ADN1test, Sequence, SequenceListe, controller, AlgorithmsStefan.launch(Sequence, SequenceListe[], boolean)

conversionFrom

public static SequenceListe[] conversionFrom(Sequence adntcible,
                                             SequenceListe[] listes,
                                             boolean diff)

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:

adntcible - (Sequence) target sequence to add in position 0

listes - (SequenceListe[])

diff - (boolean) to make a difference with conversionFrom(Sequence, SequenceListe[])

Returns:

(Vector <=> SequenceListe[]) Vector of tabs of Sequences

See Also:

ADN1test, Sequence, SequenceListe, controller, AlgorithmsStefan.launch(Sequence, SequenceListe[], boolean)

getScreenToSee

public static java.lang.String getScreenToSee(SequenceListe[] tabsadn,
                                              Sequence target,
                                              AlgorithmsStefan algo,
                                              boolean tfold)

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

Parameters:

tabsadn - (Vector) vector of tabs of palindromes

target - (Sequence)

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

Returns:

(String)

See Also:

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

afficherNom

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

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

Parameters:

tabAdn - (Sequence[])

Returns:

(String)

See Also:

getScreenToSee(SequenceListe[], Sequence, AlgorithmsStefan, boolean), getScreenToSeeHTML(SequenceListe[], Sequence, AlgorithmsStefan, boolean)

afficher_Caracteristique

private static java.lang.String afficher_Caracteristique(Sequence target,
                                                         AlgorithmsStefan algo,
                                                         boolean tfold)

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

Parameters:

target - (Sequence) target sequence

algo - (AlgorithmsStefan)

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

Returns:

(String)

See Also:

Interface3.setInterface(origincomment.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(SequenceListe[] tabsadn,
                                                  Sequence target,
                                                  AlgorithmsStefan algo,
                                                  boolean tfold)

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

Parameters:

tabsadn - (Vector) vector of tabs of palindromes

target - (Sequence)

algo - (AlgorithmsStefan)

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

Returns:

(String) HTML format vizualization...

See Also:

afficherNom_web(Sequence[])

afficherNom_web

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

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

Parameters:

tabAdn - (Sequence[])

Returns:

(String)

See Also:

getScreenToSee(SequenceListe[], Sequence, AlgorithmsStefan, boolean), getScreenToSeeHTML(SequenceListe[], Sequence, AlgorithmsStefan, boolean)

afficher_Caracteristique_Web

private static java.lang.String afficher_Caracteristique_Web(Sequence target,
                                                             AlgorithmsStefan algo,
                                                             boolean tfold)

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

Parameters:

target - (Sequence) target sequence

algo - (AlgorithmsStefan)

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

fusion_Palindrome

public static Palindrome[] fusion_Palindrome(Palindrome[] tabPalCourant,
                                             Palindrome[] 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 - (Palindrome[])

tabPalPrincipal - (Palindrome[])

Returns:

(Palindrome[])

See Also:

ArbreExec.recuperation(PalindromeListeListe, Palindrome[], NoeudArbreExec), AlgorithmsStefan.recherche_Palindrome(Sequence, int, int, int, Sequence[], 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 Sequence[] distance(Sequence target_cible,
                                   Sequence target_test,
                                   Sequence[] adntest)

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

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

Parameters:

target_cible - (Sequence) target sequence

target_test - (Sequence) target sequence

adntest - (Sequence[]) same as return ?

Returns:

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

See Also:

ConvertedProfil, trier(Sequence, Sequence[], 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 Sequence[] distance(Sequence target_cible,
                                   Sequence target_test,
                                   Sequence[] adntest,
                                   int identity,
                                   int deletion)

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

Parameters:

target_cible - (Sequence) target sequence

target_test - (Sequence) target sequence

adntest - (Sequence[]) same as return ?

identity - (int) best percentage of identity

deletion - (int) percentage of deletion

Returns:

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

See Also:

ConvertedProfil, trier(Sequence, Sequence[], int)

trier

private static Sequence[] trier(Sequence target_test,
                                Sequence[] adntest,
                                int quelscore)

To sort the tab...

Parameters:

target_test - (Sequence) (was test)

adntest - (Sequence[])

quelscore - (int)

Returns:

(Sequence[])

See Also:

distance(Sequence, Sequence, Sequence[])