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public void set prepared statement objects vector v this prepared statement objects v logger debug prepared statement objects size prepared statement objects size
set the value of prepared statement objects
public int get start servlet request request page context get request string start string request get parameter start request var if start string null logger debug start came in in request using that start try start integer parse int start string return start catch exception e logger error parsing start string failed using default return start else logger debug no start in request using default return start
get the value of start
public void set start string v this start integer parse int v
set the value of start
public void set size string v this size integer parse int v
set the value of size
public boolean get find total return find total
get the value of find total
public void set find total string v this find total v to upper case equals true
set the value of find total
public vector get errors if we have yet to hit the database so so if results null execute query return error messages
get the errors associated with this sqltag
public void add error string err error messages add err error true
get the errors associated with this sqltag
public boolean get close connection return close connection
get the value of close connection
public void set close connection string v this close connection true equals v to upper case
set the value of close connection
public boolean get display null return display null
get the value of display null
public void set display null string v this display null v to upper case equals true
set the value of display null
public string get null value to display return null value to display
get the value of null value to display
public void set null value to display string v this null value to display v
set the value of null value to display
public void set item object o this o o
set the value of o
public void set item int i this o new integer i
set the value of o
public void set item double d this o new double d
set the value of o
public boolean get display at end return display at end
get the value of display at end
public void set display at end string v this display at end true equals v to upper case
set the value of display at end
public xmlgenerator
creates a new code xmlgenerator code instance
public void set root string node label throws exception vertex node null cdaonode view root node cdaonode view get root node get node root node node label set root node
sets the selected node as the root node
public void set delete string node label throws exception vertex node null cdaonode view root node cdaonode view get root node get node root node node label if node null selected node null this remove node
deletes the selected node including its children
public void set highlight string node label throws graph exception vertex node null cdaonode view root node cdaonode view get root node get node root node node label if node null hl nodes add node
adds the selected node to hl nodes
public void set un highlight string node label throws graph exception vertex node null cdaonode view root node cdaonode view get root node get node root node node label if node null hl nodes remove node
removes the selected node from hl nodes
public void set collapse string node label throws exception vertex node null cdaonode view root node cdaonode view get root node get node root node node label if node null collapsed nodes add node
adds the selected node to collapsed nodes
public void set expand string node label throws graph exception vertex node null cdaonode view root node cdaonode view get root node get node root node node label if node null collapsed nodes remove node
removes the selected node from collapsed nodes
public void set select string node label throws exception vertex node null cdaonode view root node cdaonode view get root node get node root node node label if node null remove all other nodes retain node cdaonode view node
selects a node and its children node and removes all other nodes
public void retain node cdaonode view node to retain throws exception 1 find the children of the node to retain set cdaonode view nodes to retain get all children node to retain if nodes to retain null 2 set node to retain set root super set root node to retain 3 remove all others of non node to retain family now node to retain is the root remove nodes node to retain nodes to retain
first finds all the children nodes of the node and adds them to
public int get num enclosed leaves cdaonode view node throws exception int num 0 list cdaonode view all leaves get all leaves node if all leaves null num all leaves size return num
gets the number of enclosed leaves of a node
private cdaoview data get cdaoview data http session http session servlet request get session cdaoview data cdao view data cdaoview data http session get attribute cdao view data if cdao view data null cdao view data new cdaoview data return cdao view data
gets cdaoview data from the session if null then initializes a new
public void on module load history add value change handler this init true
the entry point method called automatically by loading a module that
public void update input panels string ht history get token string history token gwtutilis get history token ht hash map string string params new hash map string string params gwtutilis get history token parameters ht string file name params get file name string data source type params get data source type if history token equals nexplorer data source type null mediator select source data type data source type file name
this method is called during the launch of nexplorer application
protected void on update double progress if mode fade out mode progress 1 0 progress dom set style attribute we opacity style ff double to string progress dom set style attribute we opacity style ie ie opacity attr double to string progress 100 0 ie opacity attr terminator
apply the effect implicitly called
public void delete history data string history id string url phylows cdao delete history data string id id history id my httprequest async post url id new request callback public void on error request arg0 throwable arg1 mediator show error message error in server public void on response received request arg0 response arg1 jsonarray json array jsonarray jsonparser parse arg1 get text view data client vd new view data client json array mediator update history panel vd history panel set open true
this method is called when there is a request to perform delete operation
public void initial history load string url phylows cdao load history my httprequest async get url new request callback public void on error request arg0 throwable arg1 mediator show error message error in server public void on response received request arg0 response arg1 if arg1 get status code response sc ok return jsonarray json array jsonarray jsonparser parse arg1 get text view data client vd new view data client json array mediator update history panel vd if vd get history id list size 0 history panel set open true
this method is called during the launch of nexplorer application
private string x string param name object value if value null value equals null return param name value else return
this method concatenates param name and and the value and returns the
static public mediator get instance if instance null instance new mediator return instance
returns the instance of the mediator class
public void register image panel hot spots img with hot spots this set img with hot spots img with hot spots
registers image panel
public void on resize resize event resize event mediator resize main content size
this method is the implementation of resize handler that is fired when the
public void register input options input options input options this input options input options
registers input options
public void register save history panel save history panel save history panel this save history panel save history panel
registers save history panel
public void register history panel history panel history panel this history panel history panel
registers history panel
public void show ajax loader string l boolean show glass panel if loading panel null loading panel set info content l show glass panel if show glass panel message panel set visible false images panel set visible true
updates the loading panel message
public void show error message string l message panel set visible true message panel set error message l images panel set visible false show ajax loader false save history panel set visible false
this method is called when an error occurs
public void set query control query text area string query string query controls update query text area query string
sets query control text area
public void set yzoom float d uiparameter config get instance set vertical spacing d load images
this method is called when edge thickness is changed in the
public void set xzoom float f uiparameter config get instance set tree width f load images
this method is called when tree width is changed either by vertical
public void set layout string layout uiparameter config get instance set layout layout load images
this method is called when a layout is selected such as rectangular
public void set selected character matrix name string charactersame uiparameter config get instance set selected character matrix name charactersame load images
this method is called when there is characters data for a particular file
public void set selected tree name string tree name uiparameter config get instance set selected tree name tree name load images
this method is called when there is tree data for a particular file
public void set selected view options string view option uiparameter config get instance set selected view options view option load images
when both tree and characters data is present this method is called to
public void update image panel view option boolean show tree boolean show matrix images panel update view option show tree show matrix
updates image panel based on view option selected tree only characters
public void update layout otion boolean show tree boolean show matrix plot controls update layout show tree show matrix
updates layout option for tree only data character only data and tree
public void set line thickness int line thickness uiparameter config get instance set line thickness line thickness load images
changes line thickness
public void draw border boolean b plot controls is border selected uiparameter config get instance set draw border b load images
draws a border to the image
public void show right justify label boolean b plot controls is right justify selected uiparameter config get instance set right justify label b load images
sets the labels to right justified
public void load selected tree string selected tree name uiparameter config get instance set selected tree name selected tree name load images
this method is called when a new tree is selected
public void load images deferred command add command new command public void execute main load cdaoimages
this method is used to call load cdaoimages method in the nexplorer
public void load images string file name uiparameter config get instance set selected tree name file name load images
this method is called when any tree modification is performed using
public void reset tree matrix list box this data controls reset
resets data options
public void refresh data control query results list string title list if data controls null data controls refresh protein family list title list
refreshs protein family list
public void highlight node string node uri uiparameter config get instance set do action highlight uiparameter config get instance set selected node uri node uri load images
sets the node and the children highlighted
public void unhighlight node string node uri uiparameter config get instance set do action un highlight uiparameter config get instance set selected node uri node uri load images
sets the node and the children un highlighted
public void delete node string node uri uiparameter config get instance set do action delete uiparameter config get instance set selected node uri node uri load images
removes the node and its children
public void select node string node uri uiparameter config get instance set do action select uiparameter config get instance set selected node uri node uri load images
selects the node and its children other nodes do not show
public void collapse node string node uri uiparameter config get instance set do action collapse uiparameter config get instance set selected node uri node uri load images
collapses the node and its children
public void expand node string node uri uiparameter config get instance set do action expand uiparameter config get instance set selected node uri node uri load images
expands the collapsed node and its children
public void reset string node uri uiparameter config get instance set do action reset uiparameter config get instance set selected node uri node uri system out println reset mediator node uri load images
collapses the node and its children
public void print link string node uri uiparameter config get instance set do action print link uiparameter config get instance set selected node uri node uri load images
collapses the node and its children
public void swap nodes string node uri uiparameter config get instance set do action swap nodes uiparameter config get instance set selected node uri node uri system out println inside swap nodes in mediator node uri load images
swap children nodes
public void hide columns int start index int end index uiparameter config get instance set do action hide columns uiparameter config get instance set hide col start index start index uiparameter config get instance set hide col end index end index todo if no tree reload only seq alignment image load images
this method is called to hide selected columns in the sequence
public void reveal int index uiparameter config get instance set do action reveal uiparameter config get instance set reveal index index load images
reveals selected column in the sequence alignment
public void reveal all uiparameter config get instance set do action reveal all load images
reveals all columns in the sequence alignment
public void reveal sequence int index uiparameter config get instance set do action reveal sequence uiparameter config get instance set reveal index index load images
reveals row in the sequence alignment
public void reveal all sequences uiparameter config get instance set do action reveal all sequences load images
reveals all rows in the sequence alignment
public void update panels view data client vd images panel update vd data controls update vd plot controls update vd display controls update vd sequence alignment controls update vd
updates all the panels after the response is received from the server
public void update history panel view data client vd history panel update vd
updates history panel after the response is received from the server
public void read owlfile string file name model model string name space input stream in file manager get open file name check unavailability if in null system out println user dir system get property user dir throw new illegal argument exception file file name not found read the rdf xml file model read in name space
check the existence of the rdf file and read it into the model
public void update history list main initial history load
this method is called to during the launch of nexplorer application and
public void print summary cdaoutils print summary resource
prints the triples related to this node resource
public void update data control list box boolean updated data controls update list box if updated load images
updates listboxes in the data options section
public string to newick cdaonode root node cdaonode this get root if root node null return to string else system out println only rooted nodes are processed now return null
converts the tree to newick formatted tree string
public void select source data type string data source type string file name if data source type null data source type trim length 0 return input options select source data type data source type file name
this method is called to select the data source type and filename
public void reset all panels view data client vd new view data client set query options vd get query result list images panel update vd data controls update vd
this method is called to reset all panels
public void load history data string history id main load history data history id
this method is called when a history item is selected from history panel
public void delete history data string history id main delete history data history id
this method is called when there is a request to perform delete operation
public void save history string title string description string history id main save history title description history id
this method is called when save history button is clicked to save the
private void set rsl library xml configuration configuration project project flex project auxiliary configuration conf project get lookup lookup flex project auxiliary configuration class list flex library libraries conf get runtime libraries list file object list new array list file object for int ix 0 ix libraries size ix file object swc libraries get ix get swc files for int ix2 0 ix2 swc length ix2 list add swc ix2 configuration set rsl library paths to array list
a list of runtime shared library urls to be loaded before applications start
public void set class name string full class name class name full class name
main class with full classname package
public boolean is shared dependency return is shared
if it is shared library or a static
public void set compatibility version specification version version source version version
sets the sdk compatibility version
public void set theme file object files this theme files
sets a list of css or swc files to apply as a theme
public void include libraries file object libraries this libraries libraries
includes a list of swc files to completely include in the application
public flex specification get specification return specification
returns the version of the flex specification e
public void initialize wizard descriptor wizard descriptor this wizard descriptor wizard descriptor index 0 panels create panels final string step names create step names sets name for each component to be displayed into the list of step left side for int ix 0 ix panels length ix wizard descriptor panel panel panels ix jcomponent jc jcomponent panel get component jc put client property wizard panel content selected index ix noi18 n jc put client property wizard panel content data step names noi18 n jc set name step names ix to be displayed at the top of panel
init when a new flex project is choosen
protected void fire event change support fire change
when it call from xxx visual it warns panel configure projects parent
public void read wizard descriptor wizard descriptor wizard descriptor wizard descriptor final string project name string wizard descriptor get property new flex project wizard iterator prop project name final file projects location file wizard descriptor get property new flex project wizard iterator prop projects location if project name null set project name project name if projects location null set projects location projects location else set projects location project chooser get projects folder
reads properties from wizard descriptor and init user interface with them
public void store wizard descriptor wizard descriptor string project name get project name string project location get projects location string project folder get project folder wizard descriptor put property new flex project wizard iterator prop project name project name wizard descriptor put property new flex project wizard iterator prop projects location new file project location wizard descriptor put property new flex project wizard iterator prop project folder new file project folder wizard descriptor put property new flex project wizard iterator prop ref flex sdk target flex sdk get selected item
gets all properties from user interface and set them into wizard descriptor
private void init board put 0 new array list player board put 1 new array list player board put 2 new array list player
init the match
public void play player player board box board box if playing player try board get board box get x get board box get y catch index out of bounds exception e yeah i do not like ifs x d board get board box get x add player finish hand else throw new runtime exception it s not your turn
make a game play