input stringlengths 10 828 | output stringlengths 5 107 |
|---|---|
public void set value data handler value this value value | sets the value of the value property |
public retrieve document set request type create retrieve document set request type return new retrieve document set request type | create an instance of |
public retrieve document set response type create retrieve document set response type return new retrieve document set response type | create an instance of |
protected void convert from ian throws exception dataset ref series seq ian get item tags ref series seq dcm element ref sopseq ref series seq get tags ref sopseq file info aa retrieve cmd create ref sopseq get file infos file infos new array list file info aa length for file info a aa for file info fi a if is local re... | convert to file infos |
public list find gpwlentries dataset search ds if is local return find gpwlentries local search ds else return find gpwlentries from aet search ds | get a list of work list entries |
public int find mwlentries dataset search ds list result log debug query mwl scp called aet with keys log debug search ds if is local return find mwlentries local search ds result else return find mwlentries from aet search ds result | get a list of work list entries |
public boolean is matching key not supported return find unsupported matching key keys matching keys | check if this query cmd use an unsupported matching key |
public int compare to object o file info fi2 file info o int diff avail availability fi2 availability return diff avail 0 diff avail fi2 pk pk 1 1 | this will make sure the most available and for files with equal |
public boolean is matching key not supported return other patient idmatch not supported super is matching key not supported | check if this query cmd use an unsupported matching key |
public void update attributes dataset new attrs boolean overwrite req attr sq dataset old attrs get attributes false boolean updated update series request old attrs new attrs overwrite req attr sq if old attrs null set attributes new attrs else attribute filter filter attribute filter get series attribute filter if att... | update series attributes and series request |
public token authorize string auth object data throws jsonexception gsauthorization exception for authorizer a this authorizers if a is applicable to auth return a authorize auth data successfully authorized no exception raised throw new gsauthorization exception applicable authorizer not found | tries to authorize given data with first applicable |
private void check authorize header string auth throws jsonexception if auth null fixme anyone how can we return http 401 instead throw new jsonwrapped exception security msgs authorization needed if auth trim starts with json auth type fixme anyone how can we return http 401 instead throw new jsonwrapped exception sec... | checks whether given authorize header can be handled by this authorizer |
protected boolean is default factory property descriptor desc return jsonfield decl factory class get class equals desc get annotation jsonfield class factory get class | check if annotation points to default factory |
public jsonobject marshall jsonmarshaller marshaller object instance jsonobject obj throws jsonexception property descriptor collection object desc get descriptor collection object value inst desc get value instance if value inst null obj put desc get name jsonobject null else jsonarray array new jsonarray int index 0 ... | marshall collection as json encoded array |
public object unmarshall jsonmarshaller marshaller object instance jsonobject obj throws jsonexception property descriptor location desc get descriptor desc set value instance location marshaller unmarshall new location obj get jsonobject desc get name return instance | todo not tested anywhere yet |
protected jsonobject rest post call string relative resource path jsonobject data throws gsrest failed exception gsrest returned error exception gscontext not initialized exception http post post build post relative resource path data return extract value execute request post | prepares http post request with given data in body to be executed |
protected jsonarray rest post call array string relative resource path jsonobject data throws gsrest failed exception gsrest returned error exception gscontext not initialized exception http post post build post relative resource path data return extract value array execute request post | same as rest post call string jsonobject but extracts |
protected jsonobject rest get call string relative resource path throws gsrest failed exception gsrest returned error exception gscontext not initialized exception return rest get call gscontext get pref gscontext prefs server url to string relative resource path | prepares http get request to be executed |
protected jsonobject extract value string response throws gsrest failed exception gsrest returned error exception try jsonobject resp js new jsonobject response if ok equals resp js get string result return resp js get jsonobject value else jsonobject msg js resp js get jsonobject value throw new gsrest returned error ... | processes server response and extracts returned value or error message |
protected jsonarray extract value array string response throws gsrest failed exception gsrest returned error exception try jsonobject resp js new jsonobject response if ok equals resp js get string result return resp js get jsonarray value else jsonobject msg js resp js get jsonobject value throw new gsrest returned er... | same as extract value string but this one extracts value as |
protected jsonobject marshall object obj throws gsrest failed exception try return gscontext get marshaller marshall obj new jsonobject catch jsonexception e log e logtag jsonexception raised during account marshalling e throw new gsrest failed exception e | wrapper for general marshaller |
protected void set listeners new button click listener btn new set on click listener new view on click listener override public void on click view arg0 new event btn search set on click listener new view on click listener override public void on click view arg0 toast make text list events this r string msg not implemen... | takes care of setting up all list events listeners |
protected void new event intent edit event new intent edit event set class name org geoscheduler android org geoscheduler android activities edit event start activity for result edit event dbchange | starts activity to create new event |
protected repeat type get selected repeat type switch spn rep type get selected item position case 0 return repeat type weekly case 2 return repeat type daily case 3 return repeat type monthly case 4 return repeat type yearly default return repeat type once | evaluate proper code for selected repeat type |
protected void set repeat type sel index repeat type rt if rt repeat type weekly spn rep type set selection 0 else if rt repeat type daily spn rep type set selection 2 else if rt repeat type monthly spn rep type set selection 3 else if rt repeat type yearly spn rep type set selection 4 else if rt repeat type once spn r... | set proper repeat type selection index |
protected alert type get selected alert type if cb any tim is checked if spn evn locations get selected item position 0 return alert type location if edt tag get text to string equals return alert type tag fixme paja exception should be thrown here return alert type tag else if spn evn locations get selected item posit... | evaluate proper alert type for selected options |
protected void update tags string tag text edt tag get text to string string tags tag text split if current event get tags null current event set tags new array list tag else current event get tags clear for int i 0 i tags length i tags i tags i trim sqlite database db dbhelper open db this tag tag dbhelper fetch tag d... | update tags from text edit control to current event instance |
protected void select tab int tab id set tab tab main btn tab main tab id r id ee tab main set tab tab adv btn tab adv tab id r id ee tab advanced | takes care of showing up tab given by id |
protected void set tab linear layout tab image button tab btn boolean visible if visible tab set visibility view visible linear layout layout params margins new linear layout layout params 65 56 margins set margins 0 1 0 0 tab btn set layout params margins tab btn set background resource r drawable tab active else tab ... | sets state of a single tab |
protected void select on map boolean has location current event get location null update location presence intent map select new intent map select set class name org geoscheduler android map overview class get name map select put extra map overview extra map select mode 1 if has location map select put extra edit event... | select custom location on the map view |
protected void select here location manager lm location manager get system service context location service boolean wasok false if lm null android location location loc lm get last known location fixed location provider if loc null wasok true double lat loc get latitude 1 e6 double lon loc get longitude 1 e6 current ev... | select current location as the event location |
protected void update location presence if spn evn locations get selected item position 0 current event set location null else if current event get location null location tmp loc new location null 0 null null null null current event set location tmp loc select here | update presence of location on current event |
protected void update radius update location presence if current event get location null radius list is fixed yet switch spn evn radius units get selected item position case 0 current event get location set radius 500 break case 1 current event get location set radius 1000 break case 2 current event get location set ra... | update current radius value if location is selected |
public string to string final string tab string ret value ret value server statistics vo super to string tab jvm statistics this jvm statistics tab return ret value | constructs a code string code with all attributes in name value |
public void start server logger info server is starting set start time new java util date system current time millis is started is started | this method starts the server and record the start time |
public void stop server logger info thread is stoping set stop time new java util date system current time millis is started is started | this method stops the server and record the stop time |
public void show start stop time logger info making the attributes visible show details show details | shows the server details if it is not visible |
public void hide start stop time logger info hiding the attributes show details show details | hides the server details if it is visible |
protected boolean is use strict casing return use strict casing | return whether strict casing for attributes is enabled |
protected integer get default currency time limit return this default currency time limit | return default value for the jmx field currency time limit if any |
public void set registration behavior name string registration behavior set registration behavior constants as number registration behavior int value | set the registration behavior by the name of the corresponding constant |
public void remove mbeans unregister mbeans | unregisters all the registered mbeans |
protected boolean is expose class descriptor return expose class descriptor | return whether to expose the jmx descriptor field class for managed operations |
protected void on register object name object name | called when an mbean is registered under the given |
protected void on unregister object name object name | called when an mbean is unregistered under the given |
public string get show page url http servlet request request string page return request get context path request get servlet path action show page page page | returns a url suitable for redirecting to a jsp page |
protected model mbean create model mbean throws mbean exception return this expose managed resource class loader new generic model mbean new required model mbean | create an instance of a class that implements code model mbean code |
private void init user actions actions new hashtable string action actions put user actions logout new logout action actions put user actions login new login action actions put user actions authenticate new authenticate action actions put user actions show page new show page action actions put user actions jamon admin ... | put all the handlers for user interaction |
private boolean is authenticated http servlet request request boolean is authenticated false http session session request get session if session get attribute misc valid user null is authenticated true return is authenticated | returns true if the session contains the authentication token |
public void decrease nesting level this type indexes per level remove new integer this nesting level this nesting level | decrease this parameters nesting level |
protected boolean is mbean class bean class return jmx utils is mbean bean class | determine whether the given bean class qualifies as an mbean as is |
public object as object string code throws constant exception string code to use code to upper case object val this field cache get code to use if val null throw new constant exception this class name code to use not found return val | parse the given string upper or lower case accepted and return |
public void set type index for current level int type index this type indexes per level put new integer this nesting level new integer type index | set the type index for the current nesting level |
public string to code object value string name prefix throws constant exception string prefix to use name prefix to upper case for iterator it this field cache entry set iterator it has next map entry entry map entry it next string key string entry get key if key starts with prefix to use entry get value equals value r... | look up the given value within the given group of constants |
public integer get type index for level int nesting level return this type indexes per level get new integer nesting level | return the type index for the specified nesting level |
public string property to constant name prefix string property name string buffer parsed prefix new string buffer for int i 0 i property name length i char c property name char at i if character is upper case c parsed prefix append parsed prefix append c else parsed prefix append character to upper case c return parsed... | convert the given bean property name to a constant name prefix |
public throwable get root cause throwable cause get cause if cause instanceof nested runtime exception throwable root cause nested runtime exception cause get root cause return root cause null root cause cause else return cause | retrieve the innermost cause of this exception if any |
public throwable get root cause throwable cause get cause if cause instanceof nested checked exception return nested checked exception cause get root cause else return cause | retrieve the innermost cause of this exception if any |
public boolean contains class ex type if ex type null return false if ex type is instance this return true throwable cause get cause if cause instanceof nested runtime exception return nested runtime exception cause contains ex type else return cause null ex type is instance cause | check whether this exception contains an exception of the given type |
public boolean contains class ex type if ex type null return false if ex type is instance this return true throwable cause get cause if cause instanceof nested checked exception return nested checked exception cause contains ex type else return cause null ex type is instance cause | check whether this exception contains an exception of the given type |
public fitness provider get copy return new two allele fitness uni gen state s forward mu back mu 0 must use the private constructor since it doesn t add xml info | called to copy information from parent to offspring individual |
public dnasequence get sequence return seq | returns the dnasequence object that this fitnes provider is using to calculate fitness |
public void reproduce all for int i 0 i get population count i reproduce i | calls reproduce on all populations |
public void initialize populations random engine rng fitness provider fitness model for population pop get pop list pop initialize rng 1 fitness model null | initialize all populations with the given random engine and fitness model |
public void set sampling strategy strategy strat int single pop num sampling strategy strat single pop single pop num | set the sampling strategy to the given value |
public fitness provider get copy return new dnafitness rng seq master site model current fitness mut mod | obtain a copy of this dnafitness object |
public collectible get collectible return pop | we just return the population itself here |
public void reproduce int i int new size get n pop get current gen number 1 pop new gen new size | calls new gen size on the population with size determined by get n |
public boolean is system out return is sys out | returns true if this object is encapsulating system |
public void shutdown tj view write properties write properties before shutting down super shutdown | called on application shutdown we write some properties to the file on shutdown |
public int get tree sample size return integer tree sample size get value | returns the current value of the tree sample size spinner |
public void read settings from xml xmlstream reader reader throws xmlstream exception tjxmlexception if reader is start element reader get local name tjxmlconstants fitness model string model xmlparseable utils get attribute for key reader tjxmlconstants type for fitness model configurator fitness conf fitness configur... | read the various settings frmo an xml file |
public int get dnasample size return integer dna sample size get value | returns the current value of the dna sample size spinner |
public boolean get sample trees return collect trees box is selected | whether we should collect trees |
public fitness provider construct fitness model random engine rng fitness provider model null for fitness model configurator conf fitness configurators if conf get identifier equals current fitness model model conf get fitness model rng return model | create and return a new fitness provider based on the current panel settings |
public void ask about last run settings string last run settings path props get property last run settings if last run settings path null string ops reload settings don t load int choice joption pane show option dialog this get frame reload settings from last run reload settings joption pane yes no option joption pane ... | asks the user if we should reload settings from the last run |
protected void fasta box state changed if fasta box is selected fasta file stem field set enabled true fasta frequency spinner set enabled true write trees too box set enabled true separate fastas box set enabled true else fasta file stem field set enabled false fasta frequency spinner set enabled false separate fastas... | called when the state of the write dna check box has changed |
public void add stream print stream new stream if streams contains new stream streams add new stream | add a new stream to the list of streams to write output to |
private void create site fitness models site model names new array list string site models new array list site model configurator site models add new const fitness configurator site models add new neutral site configurator site models add new gamma fitness configurator site models add new gen discrete configurator site... | adds a new site model configurator to the list |
public void add statistic statistic stat stat list add stat | add a new statistic to the list of statistics to emit output for |
public void set summary stream print stream file ps summary stream file ps | a a new stream for summary writing |
public void set write single fasta string fasta filestem write fasta true fasta filestem fasta filestem fas file fasta file new file fasta filestem try fasta stream new print stream fasta file catch ioexception ioe fasta stream null jframe frame treesim japp get application get main frame if frame null frame is visible... | turn on writing of sample alignments to one big file |
private demographic configurator get current configurator for demographic configurator conf demographic configurators if conf get identifier equals current demo model return conf return null | returns the currently selected configurator using the value of current demo model |
public dnasequence generate master sequence random engine rng int length mutation model mut model dnasequence master new bit set dnasequence rng length mut model return master | constructs a new master sequence and sets the current master sequence to it |
public void set master dnasequence master this master master | set the master sequence used for this site fitness model |
public boolean get write separate fastas return true return separate fastas box is selected | deprectaed we always write separate fasta files |
public aachar lookup char amino acid aa for aachar c codon aamap key set amino acid ca codon aamap get c if ca aa return c return null | reverse lookup the aachar that corresponds to the given amino acid |
public void set master dnasequence master master codons clear for int i 0 i master length 2 i 3 triplet 0 master get base char i triplet 1 master get base char i 1 triplet 2 master get base char i 2 string codon string value of triplet amino acid aa codon utils translate codon master codons add aa | change the master sequence and master codons for this site model |
public double recompute fitness dnasequence seq dnasequence master double sum 0 for int i 0 i seq length 2 i 3 int difs 0 if seq get base char i master get base char i difs if seq get base char i 1 master get base char i 1 difs if seq get base char i 2 master get base char i 2 difs if difs 0 amino acid seq aa codon uti... | compute the fitness of the given dna sequence from scratch |
public void remove tree collection listener tree collection listener tree listener if tree listeners null tree listeners remove tree listener | remove a listener from the list of listeners |
public void collect and fire collectible pop collect pop fire new tree event get last tree | sample a new tree and then notify interested parties of the event |
public void collect without firing collectible pop collect pop | sample a new tree without firing a collection event |
public boolean collect during burnin return false | dont sample these trees during the burn in period |
public double get site fitness int site dnasequence seq return 0 | this never gets called we do everything in get fitness delta |
public void set collect data boolean collect this collect data collect | if false no data will be collected even if |
public void set write separate fastas string fasta filestem write fasta true write separate fastas true fasta file stem fasta filestem | turn on writing of fasta alignments each to a separate file |
public boolean requires genealogy return true | we need ancestral info |
public void set output serializable print stream out output out | assigns an outputstream to this statistic for writing information |
public boolean show on screen log return false | theres nothing really worth reporting on the screen log |
public boolean has configuration tool return true | true if a configuration tool is available for this statistic |
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