origincomment
Class StefanErrors

java.lang.Object
  origincomment.StefanErrors

public class StefanErrors
extends java.lang.Object

Some errors got in some places of Stefan Engelen original code / implementation. In case of lack of explanations...

Linked here some copy/paste/changes.

Some questions and remarks althought :

1. Algorithms in modelisation classes, why not but reading might be difficult.
2. What are real differences between distinct classes in each case ?
   • Palindrome1, Palindrome1cible, Palindrome1test
   • ADN1, ADN1cible, ADN1test
3. Use of untyped sets of elements (Vectors), without documentation and passed it in arguments...
   • Hard to read and understand.
   • Must be casted when using an element.
   • No commentary / documentation about their use.
   • If all objects in the same set are of same type / class : why not a tab, or a super-object which contain them and with defined procedures of use of the set ?
4. Use of tables / lists sets is not optimal...
   • copy-paste of use : why not factorize (functions) ?
   • no documentation / explanations about theses tabs
   • Why not containers ?
5. [...]

Since:

August 2008

Author:

Gabriel Chandesris (2008)

See Also:

ADN1.afficher_Caracteristique_Web(), ADN1cible.afficher_Caracteristique_Web(), ADN1cible.decoupeString(String), Palindrome1cible.toString_web()

Field Summary

private boolean	bon_format
private java.lang.String[]	champs
private int	nombreSequence
(package private) double	taux_mut Not a private element of instance...
private java.lang.String	type

Constructor Summary

StefanErrors(java.lang.String nom, java.io.BufferedReader entree)
What a faboulus constructor !

Method Summary

void	aff(int[][] matrice, java.lang.String seq5, java.lang.String seq3) Not a static procedure, but could be useful to be...
void	change_taux_mut(double taux) A very single and simple procedure, but what is wrong ?
Palindrome1test[]	choisir_meilleur(int nb, Palindrome1test[] tabpal) Not a static procedure, but could be useful to be...
private void	deuxieme_astuce_a_la_con(java.lang.String alignement)
void	diviser_regner(Palindrome1cible[] tabPal, ADN1cible adn, ADN1test[] tableauSequence, int debut, int fin, int erreur, int etape, boolean plusieurs_resultats, int nb_prediction) Instance of object is given in procedure of the same instance.
boolean	est_Compatible(Palindrome1cible pal1, Palindrome1cible pal2) Is result we are waiting for is correct ?
boolean	est_Une_Base_Test(char base) Procedures which are not in the good class, in ADN / sequence and why not in Base, or in the same as the other one ?
boolean	est_Une_Base(char base) Procedures which are not in the good class, in ADN / sequence and why not in Base ?
static Palindrome1cible[]	fusion_Palindrome(Palindrome1cible[] tabPalCourant, Palindrome1cible[] tabPalPrincipal) Curious it return two tables in one, but never suym of their length, but always 400...
boolean	match(char a, char b) [...]
private java.lang.String	premiere_astuce_a_la_con(java.io.BufferedReader entree)
int	score(char troisprime, char cinqprime) Not a static procedure, but could be useful to be...
ADN1test[]	trier(ADN1test adncible, ADN1test[] adntest, int quelscore) Instance of object is given in procedure of the same instance.

Methods inherited from class java.lang.Object

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

Field Detail

taux_mut

double taux_mut

Not a private element of instance...

type

private java.lang.String type

See Also:

StefanErrors(String, BufferedReader)

bon_format

private boolean bon_format

See Also:

StefanErrors(String, BufferedReader)

nombreSequence

private int nombreSequence

See Also:

deuxieme_astuce_a_la_con(String)

champs

private java.lang.String[] champs

See Also:

deuxieme_astuce_a_la_con(String)

Constructor Detail

StefanErrors

public StefanErrors(java.lang.String nom,
                    java.io.BufferedReader entree)
             throws java.lang.Exception

What a faboulus constructor ! Exceptions... and bullshit procedures ? Dreaming of that thing ? You got it, without any explaination !
Was originally in FichierFasta class...

Parameters:

nom -

entree -

Throws:

java.lang.Exception

See Also:

premiere_astuce_a_la_con(BufferedReader), deuxieme_astuce_a_la_con(String)

Method Detail

trier

public ADN1test[] trier(ADN1test adncible,
                        ADN1test[] adntest,
                        int quelscore)

Instance of object is given in procedure of the same instance.

Parameters:

adncible - (ADN1test) <=====

adntest - (ADN1test[])

quelscore - (int)

Returns:

(ADN1test[])

See Also:

ADN1test

diviser_regner

public void diviser_regner(Palindrome1cible[] tabPal,
                           ADN1cible adn,
                           ADN1test[] tableauSequence,
                           int debut,
                           int fin,
                           int erreur,
                           int etape,
                           boolean plusieurs_resultats,
                           int nb_prediction)

Instance of object is given in procedure of the same instance.

Parameters:

tabPal - (Palindrome1cible[]) palindrome's tab

adn - (ADN1cible) <=====

tableauSequence - (ADN1test) sequence's tab

debut - (int) begin

fin - (int) end

erreur - (int) error

etape - (int) step

plusieurs_resultats - (boolean) much results

nb_prediction - (int) number of preidctions

See Also:

ADN1cible

est_Une_Base

public boolean est_Une_Base(char base)

Procedures which are not in the good class, in ADN / sequence and why not in Base ? And not very readable : why not a regular expression ?

Parameters:

base - (char)

Returns:

(boolean)

See Also:

ADN1

est_Une_Base_Test

public boolean est_Une_Base_Test(char base)

Procedures which are not in the good class, in ADN / sequence and why not in Base, or in the same as the other one ? test procedure ?

Parameters:

base - (char)

Returns:

(boolean)

See Also:

ADN1cible, est_Une_Base(char)

change_taux_mut

public void change_taux_mut(double taux)

A very single and simple procedure, but what is wrong ? What is need whith the argument ? Value does not change !

Parameters:

taux - (double) unused ?

See Also:

Appariement

score

public int score(char troisprime,
                 char cinqprime)

Not a static procedure, but could be useful to be...

Parameters:

troisprime - (char)

cinqprime - (char)

Returns:

(int) [-1 or 1]

See Also:

ADN1test

match

public boolean match(char a,
                     char b)

[...]

Parameters:

a - (char)

b - (char)

Returns:

(boolean)

See Also:

score(char, char)

aff

public void aff(int[][] matrice,
                java.lang.String seq5,
                java.lang.String seq3)

Not a static procedure, but could be useful to be...

Parameters:

matrice -

seq5 -

seq3 -

See Also:

ADN1test

choisir_meilleur

public Palindrome1test[] choisir_meilleur(int nb,
                                          Palindrome1test[] tabpal)

Not a static procedure, but could be useful to be...

Parameters:

nb - (int)

tabpal - (Palindrome1test[])

Returns:

(Palindrome1test[])

See Also:

Palindrome1test

premiere_astuce_a_la_con

private java.lang.String premiere_astuce_a_la_con(java.io.BufferedReader entree)
                                           throws java.lang.Exception

Throws:

java.lang.Exception

See Also:

StefanErrors(String, BufferedReader)

deuxieme_astuce_a_la_con

private void deuxieme_astuce_a_la_con(java.lang.String alignement)

See Also:

StefanErrors(String, BufferedReader)

est_Compatible

public boolean est_Compatible(Palindrome1cible pal1,
                              Palindrome1cible pal2)

Is result we are waiting for is correct ? And could be static as implemented... (false == false) gives... true !

Parameters:

pal1 - (Palindrome1cible)

pal2 - (Palindrome1cible)

Returns:

(boolean)

See Also:

Palindrome1cible, Palindrome1cible.traitement_Incompatibilite(Palindrome1cible[], boolean, double, int, int)

fusion_Palindrome

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

Curious it return two tables in one, but never suym of their length, but always 400... Whatever the original lengths...

Parameters:

tabPalCourant - (Palindrome1cible[])

tabPalPrincipal - (Palindrome1cible[])

Returns:

(Palindrome1cible[])