semeru/text-code-CodeSummarization · Datasets at Hugging Face

input stringlengths 10 828	output stringlengths 5 107
public void update final observable o final object arg if arg null if a expert mode notification comes in trigger the action sampling action listener if arg equals observable enum notify expert mode set options visible	this method is called whenever the observed object is changed
public string get title return define the reference set to change body of implemented methods use file settings file templates	returns a title for the step
public void add savable savable a savable i savable elements add a savable	this method adds a savable pane
public boolean is text return false to change body of implemented methods use file settings file templates	gives a boolean that indicates if the saveble is text
public void action performed final action event e set expert chk expert is selected notify observers observable enum notify expert mode	invoked when an action occurs
public void back clicked neutralize that actions that have been undertaken i timer stop set feasable to proceed true	this method will be performed when the back button is clicked
public void next clicked i timer stop ok this is it last checks before the sampling can start main information feeder get instance set position sample size i parent get position sample size chk average is selected set feasable to proceed true	this method will be performed when the next button is clicked
private void set sequence two visible final boolean b turn the gui components in visible in response to the checkbox jpan sequence two set visible b trace the action for the parent i parent set two experiments b	set the visibility status of sequence set two
private void set forward icon if i wizard index i wizard steps length 1 btn forward set icon new image icon get class get resource icons finish png btn forward set text start btn forward set tool tip text start else btn forward set icon new image icon get class get resource icons forward png btn forward set text btn forward set tool tip text next	sets the icon for the forward button
private boolean is regional sampling sampling type enum l sampling type i parent get sampling type if l sampling type sampling type enum regional return true else return false	returns whether or not the position anchor must be shown
public string get title string l title summary return l title	returns a title for the step
private void set backward icon btn back set icon new image icon get class get resource icons back png if i wizard index 0 btn back set enabled false else btn back set enabled true	sets the icon for the backward button
public document get position document experiment type enum a type document l result null switch a type case experiment l result txt sequence get styled document break case experiment two l result txt sequences two get styled document break return l result	returns the active position jtext pane by the position type enum
private void set to begin state i active wizard step null btn forward do click	set the wizard to the start panel
private void wizard finished sampling type enum l sampling type this get sampling type sampling runner runner new sampling runner l sampling type this i acceptor messenger get instance set progress indeterminate true runner start	this method is called when the wizard is finished
private void set all options visible boolean b lbl length set visible b spin length set visible b lbl iteration size set visible b spin iteration size set visible b spin start position set visible b lbl start position set visible b rdb cterm set visible b rdb nterm set visible b	this method turns all gui option fields as visible true or false
public void set title string a title sampling step i wizard index 1 i wizard steps length i active wizard step get title lbl title set text a title	set the title of the wizzard panel
public void update final observable o final object arg if arg null if a expert mode notification comes in trigger the action sampling action listener if arg equals observable enum notify expert mode action sampling action performed new action event this 1 expert call if arg equals observable enum notify fasta combobox construct fasta combobox jpan content update ui	this method is called whenever the observed object is changed
private void update sample size spin sample size set value i parent get position sample size is averaged sample size spin sample size update ui	set the sample size
public svgdocument get svg return doc	this methods gives an svg document
public sampling type enum get sampling type return main information feeder get instance get sampling type	return the sampling type
public boolean is averaged sample size return chk average is selected	returns whether or not the sampling size should be averaged
public void set sampling type final sampling type enum a sampling type main information feeder get instance set sampling type a sampling type	set the sampling type to be used
public void get info this i start position i information feeder get start position this i standard deviation i information feeder get zscore this i aa parameter matrix i information feeder get selected aa parameter matrix this i sliding window size i information feeder get sliding window size this i use sliding window i information feeder is sliding window in aa parameter this i logo heigth i information feeder get graphable height this i logo width i information feeder get graphable width	this method get all the necessary information from the main information feeder singleton
private void set options visible if i parent is expert expert mode set all visible jpan options set visible true if two positions also enable the average chkbox if i parent has two experiments chk average set visible true else chk average set visible false else jpan options set visible false	set the visibility of the options
public boolean is expert return i expert	returns the expert mode status
public void set expert final boolean a expert i expert a expert	sets the expert mode status
public document get position document experiment type enum a type return i experiment step get position document a type	returns the jtext pane from the position step panel
private void set reference annotation neutral second remove all annotation mutable attribute set attrs txt reference get input attributes style constants set font size attrs 12 style constants set bold attrs false style constants set foreground attrs color black retrieve the pane s document object styled document doc txt reference get styled document replace the style for the entire document we exceed the length of the document by 1 so that text entered at the end of the document uses the attributes doc set character attributes 0 txt reference get text length attrs false	this method sets the reference text panel to neutral gray
public void get info this i start position i information feeder get start position this i standard deviation i information feeder get zscore this i scoring type scoring type enum frequency this i pvalue i information feeder get pvalue this i fill i information feeder is fill weblogo this i negative set correction i information feeder is weblogo negative correction	this method get all the necessary information from the main information feeder singleton
public void zoom in if i fill i logo yaxis heigth math round i logo yaxis heigth 0 5 100 100 if i logo yaxis heigth 0 0 i logo yaxis heigth 1 0 this make svg	this method makes the letters in the logo larger
public void zoom out if i fill i logo yaxis heigth math round i logo yaxis heigth 1 5 100 100 if i logo yaxis heigth 1 0 i logo yaxis heigth 2 0 this make svg	this method makes the letters in the logo smaller
public int get matrix data model type if i matrix data model instanceof one sample matrix data model return one sample else if i matrix data model instanceof two sample matrix data model return two sample else assert false return 1	returns the datamodel type of the heat map table
public void get info this i start position i feeder get start position this i standard deviation i feeder get zscore this i scoring type scoring type enum frequency this i pvalue i feeder get pvalue this i negative set correction i feeder is weblogo negative correction	this method get all the necessary information from the main information feeder singleton
public void get info this i start position i information feeder get start position this i standard deviation i information feeder get zscore get the substitution matrix this i matrix i information feeder get substitution matrix this i normalized line i information feeder is conservation line normalized this i logo heigth i information feeder get graphable height this i logo width i information feeder get graphable width	this method get all the necessary information from the main information feeder singleton
public void set labels split label set text split sequences on position negative split get value string part one i peptide example substring 0 negative split get value string part two i peptide example substring negative split get value neg one label set text example part one length part one length neg two label set text example part two length part two length	this method will set the labels in the 2 negative set panel
public void set prefix final char a prefix i prefix a prefix	set the prefix for the random sampling
public void set slider bounds int min 1 int max i peptide example length 1 int init max 1 2 negative split set minimum min negative split set maximum max negative split set value init negative split set major tick spacing 5 negative split set minor tick spacing 1 negative split set paint ticks true negative split set paint labels true negative split set border border factory create empty border 0 0 10 0	this method will set the sliderbounds in the 2 negative set panel
public int get number of positions assert i experiment statistics length i experiment two statistics length return i experiment statistics length	returns the number of positions in this matrix data model
public int get number of positions return i experiment statistics length	returns the number of positions in this matrix data model
public void fill the information feeder i info feeder set graphable height jpan content get height i info feeder set graphable width jpan content get width	add elements to the main information feeder
public string get description if this horizontal return sample the average occurence of an amino acid along a protein stretch else if this terminal return sample the average occurence of an amino acid at fixed postions else if this random return sample the average occurence of an amino acid at random along a protein else if this regional return sample the average occurence of an amino acid around a given region else return no description	returns a description for this sampling type
public double get reference sd final amino acid enum a amino acid final int a index return get reference amino acid statistics a index get statistics a amino acid get standard deviation	returns the reference standard deviation for a given amino acid
public double get reference sd amino acid enum a amino acid int a index return get reference amino acid statistics a index get statistics a amino acid get standard deviation	returns the reference standard deviation for a given amino acid
public char get one letter code return i one letter code	get the one letter code for the amino acid instance
public isampling strategy get instance isampling strategy l strategy null if this prefix l strategy new prefix sampling strategy else if this all l strategy new unrestricted sampling strategy return l strategy	returns an instance of this enumtype
private void initialize try i loader new fastadbloader i loader load i file name catch ioexception e e print stack trace	private initialization method constructs the dbloader from the fasta file
public regional fasta sequence set derive regional sequence set amino acid enum a amino acid enums int a prefix int a suffix return new regional fasta sequence set a amino acid enums this a prefix a suffix	returns a regional fasta sequence set based on this fasta sequence set
public protein next protein i active protein null try i active protein i loader next protein catch ioexception e e print stack trace return i active protein	returns the next protein in line with the fasta sequence set iteration
public double get subset percentage of fasta sequence set return double get number of sequences double get parent number of sequences	returns the percentage of the partial subset within the complete set
public protein get active protein return i active protein	returns the latest active protein
public file get fasta file if i file null return i file else return new file i file name	get the file handle for the original fasta file
public int get parent number of sequences return i sequence set get number of sequences	returns the number of sequences of the parent fasta file
public void add string a entry i raw sequences add a entry	add a sequence into the raw sequence set
public void clear content i raw sequences clear	removes all sequences from the set
public void add positve regulated entity regulated entity pos i positve regulated entity add pos	add a positive regulated entity
public void count character c count amino acid factory get amino acid c	increase the counter for character c
public string get active sequence return i active sequence	returns the last used protein sequence as retrieved from the parent sequence set
public void add negative regulated entity regulated entity neg i negative regulated entity add neg	add a negativ regulated entity
public void count amino acid enum ae if i unit counter get ae null i unit counter put ae 1 0 else i unit counter put ae i unit counter get ae 1 i counter	increase the counter for character c
public double get count amino acid enum ae object o i unit counter get ae if o null return 0 else return double o	returns the count for the given amino acid enum
public double get total count return i counter	returns the total sum of all character counts
public protein get parent protein protein l result null if i sequence set instanceof fasta sequence set l result fasta sequence set i sequence set get active protein return l result	attempts to retrieve the active protein instance
private string get matrix identifier return i matrix identifier	getter for property matrix identifier
private boolean test positve set boolean positive set ok true string positive txt pos get text string pos set positive split n int length pos set 0 length for int i 0 i pos set length i if length pos set i length positive set ok false i peptide example pos set 0 if pos set 0 equals ignore case pos set length 1 i peptide example give positive set return positive set ok	this method will test the positive set
public amino acid counter get amino acid counter int a index return i amino acid counters get a index	returns the amino acid counter at the given index
public descriptive statistics get statistics final amino acid enum a amino acid descriptive statistics impl stat new descriptive statistics impl for int i 0 i i amino acid counters size i stat add value i amino acid counters element at i get percentage a amino acid stat set sequence set size int i amino acid counters element at 0 get total count return stat	private method to genereate a descriptive statistics element for a given amino acid
public int get dimension return i amino acid counters size	returns the number of amino acid couters
private boolean test negative set jtext area area to test boolean set ok true string sequence set area to test get text string set sequence set split n int length set 0 length for int i 0 i set length i if length set i length set ok false return set ok	this method will test the negative set
public double get total matrix count double result 0 for amino acid enum l amino acid enum amino acid enum values result result get amino acid count l amino acid enum return result	returns the total sum of the matrix
public double get amino acid count amino acid enum a amino acid double result 0 for amino acid counter l amino acid counter i amino acid counters result result l amino acid counter get count a amino acid return result	returns the total count for the given amino acid enum
public color enum get color name return i color	getter for the color
public void add to main information feeder add every composition to the main information feeder for int i 0 i i compositions to write size i i feeder add swiss prot composition i compositions to write get i	this method will add every composition to the feeder
public char get amino acid return i amino acid get one letter code	getter for the amino acid
public void set amino acid amino acid enum a amino acid this i amino acid a amino acid	setter for the amino acid
public void set color color enum a color this i color a color	setter for the color
public double get change scoring type enum a type if a type scoring type enum foldchange return i fold change else if a type scoring type enum percentage return i percentage change 100 else if a type scoring type enum standard deviation return i sdchange else return i frequency	this method will give the change depending on the giver scoring type enum
public void load swissprot compositions i swiss prot means i info feeder get swiss prot compositions	this method will load the different swissprot compositions
public boolean get infinite return i infinite	getter for the infinite parameter
public boolean is chart return false	gives a boolean that indicates if the saveble is a chart
public double get calulated mean return i calulated mean	getter for the calculated mean
public double get calulated mean set two return i calulated mean set two	getter for the calculated mean of the second set
public double get frequency return i frequency	getter for the frequencey
public void set calulated mean set two double a second mean i calulated mean set two a second mean i use second mean true	setter for the calculated mean of the second set
public void set infinite boolean a infinite i infinite a infinite	setter for the infinite
public double get negative set mean return i negative set mean	getter for the reference mean
public jpanel get content panel return null	this method gives a panel with the savable information
public double get standard deviation return i standard deviation	getter for the standard deviation
public int compare to object o regulated entity ent regulated entity o if ent get change i score type this get change i score type return 1 else if ent get change i score type this get change i score type return 1 return 0	this method compares one regulated entity with an other
public int get position return i position	getter for the position
public void set score type scoring type enum a score type this i score type a score type	setter for the scoring type
public object get value for amino acid final amino acid enum a amino acid enum return i aa map get a amino acid enum to change body of implemented methods use file settings file templates	returns a vector with aa substitution instances for the given amino acid enum
public double get upper confidence limit double l zscore i info feeder get zscore return i negative set mean l zscore i standard deviation	getter for the calculated upper confidence limit
public void parse release notes string l rel notes i uniprot release l rel notes substring l rel notes index of knowledgebase release 22 l rel notes index of consists i sprot release l rel notes substring l rel notes index of swiss prot release 19 l rel notes index of of l rel notes index of swiss prot release i trembl release l rel notes substring l rel notes index of tr embl release 15 l rel notes index of of l rel notes index of tr embl release	this method will parse the uniprot release notes
public double get lower confidence limit double l zscore i info feeder get zscore return i negative set mean l zscore i standard deviation	getter for the calculated lower confidence limit
public svgdocument get svg return null	this method gives a svg document if available
public boolean compare to double a threshold return a threshold i substitution value to change body of implemented methods use file settings file templates	returns whether the substitution value is higher then the given trheshold
public object get value for amino acid amino acid enum l aa return double i aa map get l aa	getter for the value for a specific aminoacid
public amino acid enum get target return i target	returns the targetted amino acid enum
public string to string return i title	to string method

public void update final observable o final object arg if arg null if a expert mode notification comes in trigger the action sampling action listener if arg equals observable enum notify expert mode set options visible

this method is called whenever the observed object is changed

public string get title return define the reference set to change body of implemented methods use file settings file templates

returns a title for the step

public void add savable savable a savable i savable elements add a savable

this method adds a savable pane

public boolean is text return false to change body of implemented methods use file settings file templates

gives a boolean that indicates if the saveble is text

public void action performed final action event e set expert chk expert is selected notify observers observable enum notify expert mode

invoked when an action occurs

public void back clicked neutralize that actions that have been undertaken i timer stop set feasable to proceed true

this method will be performed when the back button is clicked

public void next clicked i timer stop ok this is it last checks before the sampling can start main information feeder get instance set position sample size i parent get position sample size chk average is selected set feasable to proceed true

this method will be performed when the next button is clicked

private void set sequence two visible final boolean b turn the gui components in visible in response to the checkbox jpan sequence two set visible b trace the action for the parent i parent set two experiments b

set the visibility status of sequence set two

private void set forward icon if i wizard index i wizard steps length 1 btn forward set icon new image icon get class get resource icons finish png btn forward set text start btn forward set tool tip text start else btn forward set icon new image icon get class get resource icons forward png btn forward set text btn forward set tool tip text next

sets the icon for the forward button

private boolean is regional sampling sampling type enum l sampling type i parent get sampling type if l sampling type sampling type enum regional return true else return false

returns whether or not the position anchor must be shown

public string get title string l title summary return l title

returns a title for the step

private void set backward icon btn back set icon new image icon get class get resource icons back png if i wizard index 0 btn back set enabled false else btn back set enabled true

sets the icon for the backward button

public document get position document experiment type enum a type document l result null switch a type case experiment l result txt sequence get styled document break case experiment two l result txt sequences two get styled document break return l result

returns the active position jtext pane by the position type enum

private void set to begin state i active wizard step null btn forward do click

set the wizard to the start panel

private void wizard finished sampling type enum l sampling type this get sampling type sampling runner runner new sampling runner l sampling type this i acceptor messenger get instance set progress indeterminate true runner start

this method is called when the wizard is finished

private void set all options visible boolean b lbl length set visible b spin length set visible b lbl iteration size set visible b spin iteration size set visible b spin start position set visible b lbl start position set visible b rdb cterm set visible b rdb nterm set visible b

this method turns all gui option fields as visible true or false

public void set title string a title sampling step i wizard index 1 i wizard steps length i active wizard step get title lbl title set text a title

set the title of the wizzard panel

public void update final observable o final object arg if arg null if a expert mode notification comes in trigger the action sampling action listener if arg equals observable enum notify expert mode action sampling action performed new action event this 1 expert call if arg equals observable enum notify fasta combobox construct fasta combobox jpan content update ui

this method is called whenever the observed object is changed

private void update sample size spin sample size set value i parent get position sample size is averaged sample size spin sample size update ui

set the sample size

public svgdocument get svg return doc

this methods gives an svg document

public sampling type enum get sampling type return main information feeder get instance get sampling type

return the sampling type

public boolean is averaged sample size return chk average is selected

returns whether or not the sampling size should be averaged

public void set sampling type final sampling type enum a sampling type main information feeder get instance set sampling type a sampling type

set the sampling type to be used

public void get info this i start position i information feeder get start position this i standard deviation i information feeder get zscore this i aa parameter matrix i information feeder get selected aa parameter matrix this i sliding window size i information feeder get sliding window size this i use sliding window i information feeder is sliding window in aa parameter this i logo heigth i information feeder get graphable height this i logo width i information feeder get graphable width

this method get all the necessary information from the main information feeder singleton

private void set options visible if i parent is expert expert mode set all visible jpan options set visible true if two positions also enable the average chkbox if i parent has two experiments chk average set visible true else chk average set visible false else jpan options set visible false

set the visibility of the options

public boolean is expert return i expert

returns the expert mode status

public void set expert final boolean a expert i expert a expert

sets the expert mode status

public document get position document experiment type enum a type return i experiment step get position document a type

returns the jtext pane from the position step panel

private void set reference annotation neutral second remove all annotation mutable attribute set attrs txt reference get input attributes style constants set font size attrs 12 style constants set bold attrs false style constants set foreground attrs color black retrieve the pane s document object styled document doc txt reference get styled document replace the style for the entire document we exceed the length of the document by 1 so that text entered at the end of the document uses the attributes doc set character attributes 0 txt reference get text length attrs false

this method sets the reference text panel to neutral gray

public void get info this i start position i information feeder get start position this i standard deviation i information feeder get zscore this i scoring type scoring type enum frequency this i pvalue i information feeder get pvalue this i fill i information feeder is fill weblogo this i negative set correction i information feeder is weblogo negative correction

this method get all the necessary information from the main information feeder singleton

public void zoom in if i fill i logo yaxis heigth math round i logo yaxis heigth 0 5 100 100 if i logo yaxis heigth 0 0 i logo yaxis heigth 1 0 this make svg

this method makes the letters in the logo larger

public void zoom out if i fill i logo yaxis heigth math round i logo yaxis heigth 1 5 100 100 if i logo yaxis heigth 1 0 i logo yaxis heigth 2 0 this make svg

this method makes the letters in the logo smaller

public int get matrix data model type if i matrix data model instanceof one sample matrix data model return one sample else if i matrix data model instanceof two sample matrix data model return two sample else assert false return 1

returns the datamodel type of the heat map table

public void get info this i start position i feeder get start position this i standard deviation i feeder get zscore this i scoring type scoring type enum frequency this i pvalue i feeder get pvalue this i negative set correction i feeder is weblogo negative correction

this method get all the necessary information from the main information feeder singleton

public void get info this i start position i information feeder get start position this i standard deviation i information feeder get zscore get the substitution matrix this i matrix i information feeder get substitution matrix this i normalized line i information feeder is conservation line normalized this i logo heigth i information feeder get graphable height this i logo width i information feeder get graphable width

this method get all the necessary information from the main information feeder singleton

public void set labels split label set text split sequences on position negative split get value string part one i peptide example substring 0 negative split get value string part two i peptide example substring negative split get value neg one label set text example part one length part one length neg two label set text example part two length part two length

this method will set the labels in the 2 negative set panel

public void set prefix final char a prefix i prefix a prefix

set the prefix for the random sampling

public void set slider bounds int min 1 int max i peptide example length 1 int init max 1 2 negative split set minimum min negative split set maximum max negative split set value init negative split set major tick spacing 5 negative split set minor tick spacing 1 negative split set paint ticks true negative split set paint labels true negative split set border border factory create empty border 0 0 10 0

this method will set the sliderbounds in the 2 negative set panel

public int get number of positions assert i experiment statistics length i experiment two statistics length return i experiment statistics length

returns the number of positions in this matrix data model

public int get number of positions return i experiment statistics length

returns the number of positions in this matrix data model

public void fill the information feeder i info feeder set graphable height jpan content get height i info feeder set graphable width jpan content get width

add elements to the main information feeder

public string get description if this horizontal return sample the average occurence of an amino acid along a protein stretch else if this terminal return sample the average occurence of an amino acid at fixed postions else if this random return sample the average occurence of an amino acid at random along a protein else if this regional return sample the average occurence of an amino acid around a given region else return no description

returns a description for this sampling type

public double get reference sd final amino acid enum a amino acid final int a index return get reference amino acid statistics a index get statistics a amino acid get standard deviation

returns the reference standard deviation for a given amino acid

public double get reference sd amino acid enum a amino acid int a index return get reference amino acid statistics a index get statistics a amino acid get standard deviation

returns the reference standard deviation for a given amino acid

public char get one letter code return i one letter code

get the one letter code for the amino acid instance

public isampling strategy get instance isampling strategy l strategy null if this prefix l strategy new prefix sampling strategy else if this all l strategy new unrestricted sampling strategy return l strategy

returns an instance of this enumtype

private void initialize try i loader new fastadbloader i loader load i file name catch ioexception e e print stack trace

private initialization method constructs the dbloader from the fasta file

public regional fasta sequence set derive regional sequence set amino acid enum a amino acid enums int a prefix int a suffix return new regional fasta sequence set a amino acid enums this a prefix a suffix

returns a regional fasta sequence set based on this fasta sequence set

public protein next protein i active protein null try i active protein i loader next protein catch ioexception e e print stack trace return i active protein

returns the next protein in line with the fasta sequence set iteration

public double get subset percentage of fasta sequence set return double get number of sequences double get parent number of sequences

returns the percentage of the partial subset within the complete set

public protein get active protein return i active protein

returns the latest active protein

public file get fasta file if i file null return i file else return new file i file name

get the file handle for the original fasta file

public int get parent number of sequences return i sequence set get number of sequences

returns the number of sequences of the parent fasta file

public void add string a entry i raw sequences add a entry

add a sequence into the raw sequence set

public void clear content i raw sequences clear

removes all sequences from the set

public void add positve regulated entity regulated entity pos i positve regulated entity add pos

add a positive regulated entity

public void count character c count amino acid factory get amino acid c

increase the counter for character c

public string get active sequence return i active sequence

returns the last used protein sequence as retrieved from the parent sequence set

public void add negative regulated entity regulated entity neg i negative regulated entity add neg

add a negativ regulated entity

public void count amino acid enum ae if i unit counter get ae null i unit counter put ae 1 0 else i unit counter put ae i unit counter get ae 1 i counter

increase the counter for character c

public double get count amino acid enum ae object o i unit counter get ae if o null return 0 else return double o

returns the count for the given amino acid enum

public double get total count return i counter

returns the total sum of all character counts

public protein get parent protein protein l result null if i sequence set instanceof fasta sequence set l result fasta sequence set i sequence set get active protein return l result

attempts to retrieve the active protein instance

private string get matrix identifier return i matrix identifier

getter for property matrix identifier

private boolean test positve set boolean positive set ok true string positive txt pos get text string pos set positive split n int length pos set 0 length for int i 0 i pos set length i if length pos set i length positive set ok false i peptide example pos set 0 if pos set 0 equals ignore case pos set length 1 i peptide example give positive set return positive set ok

this method will test the positive set

public amino acid counter get amino acid counter int a index return i amino acid counters get a index

returns the amino acid counter at the given index

public descriptive statistics get statistics final amino acid enum a amino acid descriptive statistics impl stat new descriptive statistics impl for int i 0 i i amino acid counters size i stat add value i amino acid counters element at i get percentage a amino acid stat set sequence set size int i amino acid counters element at 0 get total count return stat

private method to genereate a descriptive statistics element for a given amino acid

public int get dimension return i amino acid counters size

returns the number of amino acid couters

private boolean test negative set jtext area area to test boolean set ok true string sequence set area to test get text string set sequence set split n int length set 0 length for int i 0 i set length i if length set i length set ok false return set ok

this method will test the negative set

public double get total matrix count double result 0 for amino acid enum l amino acid enum amino acid enum values result result get amino acid count l amino acid enum return result

returns the total sum of the matrix

public double get amino acid count amino acid enum a amino acid double result 0 for amino acid counter l amino acid counter i amino acid counters result result l amino acid counter get count a amino acid return result

returns the total count for the given amino acid enum

public color enum get color name return i color

getter for the color

public void add to main information feeder add every composition to the main information feeder for int i 0 i i compositions to write size i i feeder add swiss prot composition i compositions to write get i

this method will add every composition to the feeder

public char get amino acid return i amino acid get one letter code

getter for the amino acid

public void set amino acid amino acid enum a amino acid this i amino acid a amino acid

setter for the amino acid

public void set color color enum a color this i color a color

setter for the color

public double get change scoring type enum a type if a type scoring type enum foldchange return i fold change else if a type scoring type enum percentage return i percentage change 100 else if a type scoring type enum standard deviation return i sdchange else return i frequency

this method will give the change depending on the giver scoring type enum

public void load swissprot compositions i swiss prot means i info feeder get swiss prot compositions

this method will load the different swissprot compositions

public boolean get infinite return i infinite

getter for the infinite parameter

public boolean is chart return false

gives a boolean that indicates if the saveble is a chart

public double get calulated mean return i calulated mean

getter for the calculated mean

public double get calulated mean set two return i calulated mean set two

getter for the calculated mean of the second set

public double get frequency return i frequency

getter for the frequencey

public void set calulated mean set two double a second mean i calulated mean set two a second mean i use second mean true

setter for the calculated mean of the second set

public void set infinite boolean a infinite i infinite a infinite

setter for the infinite

public double get negative set mean return i negative set mean

getter for the reference mean

public jpanel get content panel return null

this method gives a panel with the savable information

public double get standard deviation return i standard deviation

getter for the standard deviation

public int compare to object o regulated entity ent regulated entity o if ent get change i score type this get change i score type return 1 else if ent get change i score type this get change i score type return 1 return 0

this method compares one regulated entity with an other

public int get position return i position

getter for the position

public void set score type scoring type enum a score type this i score type a score type

setter for the scoring type

public object get value for amino acid final amino acid enum a amino acid enum return i aa map get a amino acid enum to change body of implemented methods use file settings file templates

returns a vector with aa substitution instances for the given amino acid enum

public double get upper confidence limit double l zscore i info feeder get zscore return i negative set mean l zscore i standard deviation

getter for the calculated upper confidence limit

public void parse release notes string l rel notes i uniprot release l rel notes substring l rel notes index of knowledgebase release 22 l rel notes index of consists i sprot release l rel notes substring l rel notes index of swiss prot release 19 l rel notes index of of l rel notes index of swiss prot release i trembl release l rel notes substring l rel notes index of tr embl release 15 l rel notes index of of l rel notes index of tr embl release

this method will parse the uniprot release notes

public double get lower confidence limit double l zscore i info feeder get zscore return i negative set mean l zscore i standard deviation

getter for the calculated lower confidence limit

public svgdocument get svg return null

this method gives a svg document if available

public boolean compare to double a threshold return a threshold i substitution value to change body of implemented methods use file settings file templates

returns whether the substitution value is higher then the given trheshold

public object get value for amino acid amino acid enum l aa return double i aa map get l aa

getter for the value for a specific aminoacid

public amino acid enum get target return i target

returns the targetted amino acid enum

public string to string return i title

to string method