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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
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set the value of prepared statement objects
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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
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get the value of start
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public void set start string v this start integer parse int v
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set the value of start
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public void set size string v this size integer parse int v
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set the value of size
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public boolean get find total return find total
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get the value of find total
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public void set find total string v this find total v to upper case equals true
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set the value of find total
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public vector get errors if we have yet to hit the database so so if results null execute query return error messages
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get the errors associated with this sqltag
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public void add error string err error messages add err error true
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get the errors associated with this sqltag
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public boolean get close connection return close connection
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get the value of close connection
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public void set close connection string v this close connection true equals v to upper case
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set the value of close connection
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public boolean get display null return display null
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get the value of display null
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public void set display null string v this display null v to upper case equals true
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set the value of display null
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public string get null value to display return null value to display
|
get the value of null value to display
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public void set null value to display string v this null value to display v
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set the value of null value to display
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public void set item object o this o o
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set the value of o
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public void set item int i this o new integer i
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set the value of o
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public void set item double d this o new double d
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set the value of o
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public boolean get display at end return display at end
|
get the value of display at end
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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
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public xmlgenerator
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creates a new code xmlgenerator code instance
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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
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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
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deletes the selected node including its children
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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
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adds the selected node to hl nodes
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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
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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
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adds the selected node to collapsed nodes
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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
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removes the selected node from collapsed nodes
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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
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selects a node and its children node and removes all other nodes
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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
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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
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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
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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
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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
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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
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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
|
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