A B C D E F G H I J K L M N O P Q R S T U V W X Y

P

paeru - Static variable in class testsorigin.Alignedalphad

paeru - Static variable in class testssuite02.Alignedalphad

paint(Graphics) - Method in class alonecontroller.AloneApplet

Deprecated. A little Hello World.

paint(Graphics) - Method in class aloneinterfaces.MonBouton

paint(Graphics) - Method in class aloneinterfaces.MonImage

pairwise - Static variable in class modele.Alignement

To test if a pairwise has happend precedently.

palindrome - Variable in class aloneinterfaces.Interface11

Palindrome - Class in modele

This class define object which are part of sequences found in auto reverse alignment and cearching structure with positive score.

Palindrome(int, int, int) - Constructor for class modele.Palindrome

Short constructor with beginning, end and length of Palindrome.

Palindrome(int, int, int, double) - Constructor for class modele.Palindrome

The complete constructor of an Palindrome Object.

Palindrome(int, int, int, int) - Constructor for class modele.Palindrome

The complete constructor of a cible Palindrome.

Palindrome(int, int, int, int, boolean) - Constructor for class modele.Palindrome

The complete constructor of a test Palindrome.

Palindrome1 - Class in origincomment

Main class for palindromes

Palindrome1() - Constructor for class origincomment.Palindrome1

Default constructor : nothing happend.

Palindrome1(int, int) - Constructor for class origincomment.Palindrome1

Constructor with given begin and end of the palindrome.

Palindrome1cible - Class in origincomment

This define palindromes of the target sequence (sometimes from test ?).

Palindrome1cible() - Constructor for class origincomment.Palindrome1cible

Default constructor : nothing happend.

Palindrome1cible(int, int, int) - Constructor for class origincomment.Palindrome1cible

Constrcutor with given begin, end and length.

Palindrome1cible(int, int, int, int) - Constructor for class origincomment.Palindrome1cible

Constructor with given begin, end, length and criterion.

Palindrome1cible(int, int, int, int, int) - Constructor for class origincomment.Palindrome1cible

Constructor with given begin, end, length and number of mutations.

Palindrome1test - Class in origincomment

This define palindromes of test sequences ??

Palindrome1test(int, int, int, int) - Constructor for class origincomment.Palindrome1test

Constructor with given begin, end and two lengths.

PalindromeCible - Class in modele

Deprecated. Transfered to Palindrome

PalindromeCible(int, int, int) - Constructor for class modele.PalindromeCible

Deprecated.

PalindromeCible(int, int, int, double) - Constructor for class modele.PalindromeCible

Deprecated.

PalindromeListe - Class in modele

This class to provide easy-to-use Palindrome tables / Lists.

PalindromeListe() - Constructor for class modele.PalindromeListe

Default constructor with a list of 0 elements.

PalindromeListe(Palindrome[]) - Constructor for class modele.PalindromeListe

Constructor with a pre-made table of Palindrome's.

PalindromeListeListe - Class in modele

For some results of differents structures, this class is used on high level of algorithms.

PalindromeListeListe() - Constructor for class modele.PalindromeListeListe

Default constructor with a list of 0 elements.

PalindromeListeListe(PalindromeListe[]) - Constructor for class modele.PalindromeListeListe

Constructor with a pre-made table of PalindromeListe's.

palindromes - Variable in class modele.Alignement

List of the Palindrome's.

palindromes - Variable in class modele.NoeudArbreExec

The node contain a list of Palindrome's.

palindromes_communs(Palindrome[], Palindrome[], boolean) - Static method in class modele.AlgorithmsStefan

RESULT TREAMENT
"Previous method variation [comparaison_palindrome] to find common palindromes between two predictions.

palindromes_communs(Palindrome1cible[], Palindrome1cible[], boolean) - Static method in class modele.OriginAlgorithmsStefan

RESULT TREAMENT
"Previous method variation [comparaison_palindrome] to find common palindromes between two predictions.

palindromes_communs(Palindrome[], Palindrome[], boolean) - Static method in class modele.OtherAlgorithmsStefan

RESULT TREAMENT
"Previous method variation [comparaison_palindrome] to find common palindromes between two predictions.

palindromes_communs(Palindrome1cible[], Palindrome1cible[], boolean) - Static method in class origincomment.ADN1cible

RESULT TREAMENT
"Previous method variation [comparaison_palindrome] to find common palindromes between two predictions.

PalindromeTest - Class in modele

Deprecated. Transfered to Palindrome

PalindromeTest(int, int, int, int) - Constructor for class modele.PalindromeTest

Deprecated. Constructor with given begin, end and two lengths.

pamal - Static variable in class testsorigin.Alignedalphad

pamal - Static variable in class testssuite02.Alignedalphad

pamul - Static variable in class testsorigin.Alignedtmrna

pamul - Static variable in class testssuite02.Alignedtmrna

parcourir - Variable in class aloneinterfaces.Interface0

To select FASTA format file alignment.

parcourirFichier - Variable in class aloneinterfaces.Interface10

Selection button for file recording.

parcourirFichier - Variable in class aloneinterfaces.Interface2

To select optimal result file.

parcourirFichier1 - Variable in class aloneinterfaces.Interface8

parcourirFichier2 - Variable in class aloneinterfaces.Interface8

parcourirGraphique - Variable in class aloneinterfaces.Interface10

Selection button for graphic recording.

pasmul - Variable in class testssuite01.TestAlgorithmsPartIII

Pas. mul. tmRNA

pasmul - Variable in class testssuite01.TestAlgorithmsPartIV

Pas. mul. tmRNA

pere - Variable in class modele.NoeudArbreExec

Father of current node.

pere - Variable in class origincomment.NoeudPalindrome

Father of current node (default is null).

pertinence - Variable in class modele.Palindrome

Palindrome relevance [FR : pertinence].

pertinence - Variable in class origincomment.Alignement

Relevance (deafult : 1.0).

pertinence - Variable in class origincomment.Palindrome1cible

"Public attribute"
Relevance (default is 1.0).

plusieursStructures - Variable in class aloneinterfaces.Interface1

pmult - Static variable in class testsorigin.Alignedalphad

pmult - Static variable in class testssuite02.Alignedalphad

pogin - Static variable in class testsorigin.Alignedtmrna

pogin - Static variable in class testssuite02.Alignedtmrna

poid - Variable in class modele.Palindrome

Palindrome weight.

poidsequence - Variable in class modele.PalindromeCible

Deprecated. Sequence weight.

poidsequence - Variable in class origincomment.Palindrome1cible

"Public attribute"
Sequence weight.

popur - Static variable in class testsorigin.Alignedtmrna

popur - Static variable in class testssuite02.Alignedtmrna

pos3prime - Variable in class origincomment.Appariement

3' position.

pos5prime - Variable in class origincomment.Appariement

5' position.

position - Variable in class modele.Base

position - Variable in class origincomment.Base

Position.

position3prime - Variable in class origincomment.Matrice_ALN

"bases postions of palindrome in test sequence" 3' side

position5prime - Variable in class origincomment.Matrice_ALN

"bases postions of palindrome in test sequence" 5' side

positionDebut - Variable in class modele.Palindrome

Position of the Palindrome on sequence (begin and end).

positionDebut - Variable in class origincomment.Palindrome1

Begin position.

positionFin - Variable in class modele.Palindrome

Position of the Palindrome on sequence (begin and end).

positionFin - Variable in class origincomment.Palindrome1

End position.

pourcentage(int, int) - Method in class modele.ConvertedProfil

pourcentage(int, int) - Method in class origincomment.Profil

pourcentage_base() - Method in class origincomment.ADN1cible

Deprecated. [never used]

pourcentage_conservation - Variable in class modele.Palindrome

Cible : Conservation rate / percentage (default is 1).

pourcentage_conservation - Variable in class modele.PalindromeCible

Deprecated. Conservation rate / percentage (default is 1).

pourcentage_conservation - Variable in class origincomment.Palindrome1cible

"Internal attributes"
Conservation rate / percentage (default is 1).

pourcentage_Mutation(ADN1test[], int, boolean) - Method in class origincomment.ADN1cible

Deprecated. [never used]

pourcentageBases() - Method in class modele.Sequence

Sum the percentage of each nucleotide.

pputi - Static variable in class testsorigin.Alignedalphad

pputi - Static variable in class testssuite02.Alignedalphad

premiere_astuce_a_la_con(BufferedReader) - Method in class origincomment.StefanErrors

premiereSeq - Variable in class aloneinterfaces.Interface2

Interface memory.

premiereSequence - Variable in class aloneinterfaces.Interface2

First sequence text area visualization

printFile() - Method in class alonefichiers.Fichier

This method to create files.

Processus - Class in controller

Deprecated. Do not use : see changes on others before change here and use it...

Processus() - Constructor for class controller.Processus

Deprecated.

Processus_old - Class in controller

Deprecated. Conserved for memory (old version of June 2008)

Processus_old() - Constructor for class controller.Processus_old

Deprecated.

ProcessusNew - Class in controller

Attention / take care !

ProcessusNew() - Constructor for class controller.ProcessusNew

ProcessusOrigin - Class in controller

Attention / take care !

ProcessusOrigin() - Constructor for class controller.ProcessusOrigin

processusParent - Variable in class aloneinterfaces.Interface

Parent Processus.

profil - Variable in class modele.ConvertedProfil

The matrix of profile

Profil - Class in origincomment

"A mutation profile is a 4*4 matrix" : in reality it is 4*7...

Profil() - Constructor for class origincomment.Profil

Deprecated. [not used]

Profil(ADN1cible, ADN1test[]) - Constructor for class origincomment.Profil

Constrcutor with given target sequence and table of test sequences.

profil - Variable in class origincomment.Profil

The matrix of profile

PROFILHELICE - Static variable in class modele.AlgorithmsStefan

"Global attributes of work"
Helix profile is 2.

PROFILHELICE - Static variable in class modele.OriginAlgorithmsStefan

"Global attributes of work"
Helix profile is 2.

PROFILHELICE - Static variable in class modele.OtherAlgorithmsStefan

"Global attributes of work"
Helix profile is 2.

PROFILHELICE - Static variable in class origincomment.ADN1cible

"Global attributes of work"
Helix profile is 2.

progressBar - Variable in class aloneinterfaces.AloneProcessus

progressBar - Variable in class aloneinterfaces.AloneProcessus_old

psaer - Static variable in class testsorigin.Alignedtmrna

psaer - Static variable in class testssuite02.Alignedtmrna

pseudoNoeud - Variable in class aloneinterfaces.Interface1

pseudonoeud - Variable in class modele.AlgorithmsStefan

"Global attributes of work"
Current complexity of searching pseudoknots.

pseudonoeud - Variable in class modele.OriginAlgorithmsStefan

"Global attributes of work"
Current complexity of searching pseudoknots.

pseudonoeud - Variable in class modele.OtherAlgorithmsStefan

"Global attributes of work"
Current complexity of searching pseudoknots.

pseudonoeud - Variable in class origincomment.ADN1cible

"Global attributes of work"
Current complexity of searching pseudoknots.

pshal - Static variable in class testsorigin.Alignedtmrna

pshal - Static variable in class testssuite02.Alignedtmrna

psput - Static variable in class testsorigin.Alignedtmrna

psput - Static variable in class testssuite02.Alignedtmrna

psyri - Static variable in class testsorigin.Alignedalphad

psyri - Static variable in class testssuite02.Alignedalphad

putSequence(String) - Method in class modele.Sequence

Factorization of input in memory of the sequence.