controller
Class ListeBean

java.lang.Object
  modele.ObjectListe
      modele.SequenceListe
          controller.ListeBean

public class ListeBean
extends SequenceListe

This class to transmit informations to the Java Servlet Page.

Author:

Gabriel Chandesris (2008)

Field Summary

private java.lang.String	alignmentFile To get the alignment FASTA File.
private java.lang.String	bestpredictions To get the best predictions to be selected by SSCA.
private java.lang.String	bracketFile To get the result brackets File.
private Sequence	cible Better record here than in session.
private java.lang.String	contenuListe What will appear in the HTML form selection of following pages : .
private java.lang.String	contenuListeJavaScript To provide selection and view in web interface (JavaScript power !).
private java.lang.String	contenuListeMore What will appear in the HTML form selection of following page : .
private java.lang.String	homoResults Results for homologuous results to appear in formselectionhomol.jsp.
private SequenceListe[]	more To get the many combinations selected after SSCA.
private int	n The optimal number of sequences in a prediction.
private int	nombreSequences Number of sequences (can be useful to control number of sequences in alignment).
private java.lang.String	results To get the results in text / plain format
private java.lang.String	rnavizFile To get the result RnaViz File.
private java.lang.String	SSCAResult To get the results of SSCA

Constructor Summary

ListeBean()

Method Summary

void	addToResults(java.lang.String moreResults) To add some more information to results (i.e. parameters...)
void	computeContenuListe() This procedure to compute the contenuListe to be correct.
void	computeEffectsInContenuListe() This procedure to compute results of SSCA algorithms (effects) Black Box note : scores *(-1)
SequenceListe[]	computePredictions() To compute and gain all possible predictions (combinations).
SequenceListe[]	computePredictionsBB() Deprecated. putted when conversion ProcessusOrigin.conversionFrom(origincomment.ADN1test, SequenceListe[])
void	computePredictionsListes(int n) This procedure to compute the differents predictions, which can be selected.
private void	computeSSCAresults() This to permit export of SSCA results in XML format.
private static java.lang.String	convertNom(java.lang.String nom) This procedure to remove first ('>') and last ('\n') character in sequences' names.
private static java.lang.String	decoupeString(java.lang.String chaineDecoupe) This method to cut a String by 80 characters length substring.
java.lang.String	getAlignmentFile() To get the alignment in fasta format and as a String.
java.lang.String	getBestpredictions() To get the output in HTML format for best predictions of SSCA.
java.lang.String	getBracketFile() The content of results in bracket file format in String.
Sequence	getCible() To get the target sequence.
java.lang.String	getContenuListe() To get the output in HTML format of what the list contain for selection.
java.lang.String	getContenuListeJavaScript() To get the output in HTML/JavaScript format of what the list contain for selection.
java.lang.String	getContenuListeMore() To get the output in HTML format of what the list contain for selection.
java.lang.String	getHomoResults() To get the output in HTML format for homologuous results to appear in formselectionhomol.jsp.
static java.lang.String	getMinicadre(boolean logo) Deprecated. [see the include]
SequenceListe[]	getMore(boolean tfold) To get the many combinations selected after SSCA.
int	getN()
int	getNombreSequences() To get the number of sequences.
int	getNT()
java.lang.String	getResults() Use on page exportresults.jsp.
java.lang.String	getRnavizFile() The content of results in RnaViz file format in String.
java.lang.String	getSSCAResult() The content of SSCA sresult ins a XML String format.
void	setCible(int cible) To record the target sequence.
void	setCible(Sequence cible) To record the target sequence.
void	setN(int n)
void	setResults(Sequence cible, PalindromeListeListe results) This procedure to compute the RnaViz and Bracket file result.
void	setResults(java.lang.String results) To set the text / plain results.

Methods inherited from class modele.SequenceListe

addSequence, clone, combinationWithoutRepetition, combinatoire, computeAverageVariabilite, equals, factorielle, getListe, getMoyenneVariabilite, getSequence, getSequence, has, isIn, length, removeSequence, removeSequence, setListe, setSequence, sortByDecreasing, sortByIncreasing

Methods inherited from class modele.ObjectListe

addObjet, equals, getListeObjects, getObject, has, removeObject, removeObject, setListe, setObject

Methods inherited from class java.lang.Object

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

Field Detail

contenuListe

private java.lang.String contenuListe

What will appear in the HTML form selection of following pages : .
formselectioncible.jsp (for target sequence selection)
formselectioncibleonly.jsp (for target sequence selection)
formselectionhomol.jsp

Since:

June 2008

contenuListeJavaScript

private java.lang.String contenuListeJavaScript

To provide selection and view in web interface (JavaScript power !).
formselectioncibleonly.jsp (for target sequence selection)

Since:

September 2008

contenuListeMore

private java.lang.String contenuListeMore

What will appear in the HTML form selection of following page : .
formselectioncible.jsp (for P-DCFold multiple selection)

Since:

August 2008

nombreSequences

private int nombreSequences

Number of sequences (can be useful to control number of sequences in alignment).

Since:

June 2008

homoResults

private java.lang.String homoResults

Results for homologuous results to appear in formselectionhomol.jsp.

Since:

June 2008

cible

private Sequence cible

Better record here than in session.

Since:

July 2008

results

private java.lang.String results

To get the results in text / plain format

Since:

September 2008

See Also:

OriginAlgorithmsStefan.getResults()

rnavizFile

private java.lang.String rnavizFile

To get the result RnaViz File.

Since:

July 2008

bracketFile

private java.lang.String bracketFile

To get the result brackets File.

Since:

July 2008

alignmentFile

private java.lang.String alignmentFile

To get the alignment FASTA File.

Since:

July 2008

SSCAResult

private java.lang.String SSCAResult

To get the results of SSCA

Since:

July 2008

bestpredictions

private java.lang.String bestpredictions

To get the best predictions to be selected by SSCA.

Since:

July 2008

more

private SequenceListe[] more

To get the many combinations selected after SSCA.

Since:

July 2008

See Also:

computePredictions(), getMore(boolean)

n

private int n

The optimal number of sequences in a prediction.

Since:

July 2008

Constructor Detail

ListeBean

public ListeBean()

Method Detail

computeContenuListe

public void computeContenuListe()

This procedure to compute the contenuListe to be correct.

Since:

June 2008

See Also:

contenuListe, contenuListeMore, nombreSequences, getContenuListe(), getNombreSequences()

computePredictions

public SequenceListe[] computePredictions()

To compute and gain all possible predictions (combinations).

Returns:

(SequenceListe[])

Since:

August 2008

See Also:

SequenceListe.combinationWithoutRepetition(int, int, SequenceListe)

computePredictionsBB

public SequenceListe[] computePredictionsBB()

Deprecated. putted when conversion ProcessusOrigin.conversionFrom(origincomment.ADN1test, SequenceListe[])

To compute and gain all possible predictions (combinations) for Black Box : i.e. target sequence at position 0 in combination of sequences submitted to BB.

Returns:

(SequenceListe[])

Since:

August 2008

See Also:

SequenceListe.combinationWithoutRepetition(int, int, SequenceListe), ProcessusOrigin.conversionFrom(origincomment.ADN1test, SequenceListe[])

computePredictionsListes

public void computePredictionsListes(int n)

This procedure to compute the differents predictions, which can be selected.

Parameters:

n - (int) Optimal number of sequences to be selected in the Liste.

Since:

July 2008

See Also:

bestpredictions, getBestpredictions(), SequenceListe.combinationWithoutRepetition(int, int, SequenceListe), computePredictions()

computeEffectsInContenuListe

public void computeEffectsInContenuListe()

This procedure to compute results of SSCA algorithms (effects)
Black Box note : scores *(-1)

Since:

June 2008

See Also:

homoResults, getHomoResults(), computeSSCAresults()

computeSSCAresults

private void computeSSCAresults()

This to permit export of SSCA results in XML format.

Since:

July 2008

See Also:

SSCAResult, computeEffectsInContenuListe()

convertNom

private static java.lang.String convertNom(java.lang.String nom)

This procedure to remove first ('>') and last ('\n') character in sequences' names.

Parameters:

nom - (String)

Returns:

(String)

See Also:

computeSSCAresults()

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)

See Also:

Processus.doPost(HttpServletRequest, HttpServletResponse)

getMinicadre

public static java.lang.String getMinicadre(boolean logo)

Deprecated. [see the include]

To return the left list of links on Servlet pages .

Parameters:

logo - (boolean) to get logo or not

Returns:

(String) HTML format.

getContenuListe

public java.lang.String getContenuListe()

To get the output in HTML format of what the list contain for selection.

Returns:

(String)

Since:

June 2008

See Also:

contenuListe, computeContenuListe()

getContenuListeJavaScript

public java.lang.String getContenuListeJavaScript()

To get the output in HTML/JavaScript format of what the list contain for selection.

Returns:

(String)

Since:

September 2008

See Also:

contenuListeJavaScript, computeContenuListe()

getContenuListeMore

public java.lang.String getContenuListeMore()

To get the output in HTML format of what the list contain for selection.

Returns:

(String)

Since:

June 2008

See Also:

contenuListeMore, computeContenuListe()

getNombreSequences

public int getNombreSequences()

To get the number of sequences.

Returns:

(int)

Since:

June 2008

See Also:

nombreSequences

getHomoResults

public java.lang.String getHomoResults()

To get the output in HTML format for homologuous results to appear in formselectionhomol.jsp.

Returns:

(String)

Since:

June 2008

See Also:

homoResults, computeEffectsInContenuListe()

getBestpredictions

public java.lang.String getBestpredictions()

To get the output in HTML format for best predictions of SSCA.

Returns:

(String)

Since:

July 2008

See Also:

bestpredictions, computePredictionsListes(int)

getMore

public SequenceListe[] getMore(boolean tfold)

To get the many combinations selected after SSCA.

Parameters:

tfold - (boolean) to precise if TFold of P-DCFold launched

Returns:

SequenceListe[]

Since:

July 2008

See Also:

more, computePredictions()

getAlignmentFile

public java.lang.String getAlignmentFile()

To get the alignment in fasta format and as a String.

Returns:

(String)

Since:

July 2008

See Also:

alonefichiers

setResults

public void setResults(Sequence cible,
                       PalindromeListeListe results)

This procedure to compute the RnaViz and Bracket file result.

Parameters:

cible - (Sequence)

results - (PalindromeListeListe)

Since:

July 2008

See Also:

rnavizFile, bracketFile, alonefichiers, alonefichiers

setResults

public void setResults(java.lang.String results)

To set the text / plain results.

Parameters:

results - (String)

Since:

September 2008

See Also:

OriginAlgorithmsStefan.getResults()

addToResults

public void addToResults(java.lang.String moreResults)

To add some more information to results (i.e. parameters...)

Parameters:

moreResults - (String)

getResults

public java.lang.String getResults()

Use on page exportresults.jsp.

Returns:

(String) text/plain

Since:

September 2008

getRnavizFile

public java.lang.String getRnavizFile()

The content of results in RnaViz file format in String.

Returns:

(String)

Since:

July 2008

See Also:

setResults(Sequence, PalindromeListeListe)

getBracketFile

public java.lang.String getBracketFile()

The content of results in bracket file format in String.

Returns:

(String)

Since:

July 2008

See Also:

setResults(Sequence, PalindromeListeListe)

getSSCAResult

public java.lang.String getSSCAResult()

The content of SSCA sresult ins a XML String format.

Returns:

(String)

Since:

July 2008

See Also:

SSCAResult, computeSSCAresults()

setCible

public void setCible(int cible)

To record the target sequence.

Parameters:

cible - (Sequence)

Since:

July 2008

See Also:

cible

setCible

public void setCible(Sequence cible)

To record the target sequence.

Parameters:

cible - (Sequence)

Since:

July 2008

See Also:

cible

getCible

public Sequence getCible()

To get the target sequence.
(null if not setted).

Returns:

(Sequence)

getN

public int getN()

setN

public void setN(int n)

getNT

public int getNT()