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

input stringlengths 10 828	output stringlengths 5 107
protected void set db name string db name this db name db name	set the db username
public void test create sub organization throws exception iorganization parent factory get organization org1 name iorganization organization factory create organization org2 name sql organization parent get id assert not null organization	test number 8
public string get options string key string subkey return templatized value return get options key subkey true	get the name of the next stage in the pipeline
protected string get db passwd if db passwd null db passwd get info get str value db passwd return db passwd	get the db password
protected void set db passwd string db passwd this db passwd db passwd	set the db password
public void test create user high level throws exception user user new sql user user2 name password user credential credential new password user credential password iuser context context factory create user user credential assert not null context factory delete user user	test number 4 creation of users using high level interface
private void release connection connection conn throws config exception try if cache connection conn close catch sqlexception e throw new config exception i18n get sql 109 e	release connection called to release the connection object
protected string get db url if db url null db url get info get str value db url return db url	get the db url
protected void set db url string db url this db url db url	set the db url
public void add resource user resource user resource throws user exception this add resource user resource iuser null	add resource add a resource
public void test create user low level throws exception iuser context context factory create user user1 name password assert not null context	test number 1 test low level user creation
protected string get db driver if db driver null db driver get info get str value db driver return db driver	get the db driver
public void test delete global preferences throws exception factory delete global preference preference1 factory delete global preference preference2	test number 13
public iconfig get config string name locale locale string country locale get country string language locale get language if country null name country if language null name language return get config name	get child a config bundle for the name and given locale
private connection get connection throws resource exception if resource null resource resource factory get resource this get options resource name if resource null throw new resource exception i18n get sql 103 return connection resource check out	get the named resource name from the resource factory
public void test delete org preferences throws exception iorganization org factory get organization org2 name factory delete organization preference org preference1 factory delete organization preference org preference2	test number 16
public void execute command line command line if command line has option d string dir command line get option value d directory new file dir if directory is directory this sql config service new sql config service process directory else system err println i18n get sql 004 dir else print usage	handle the command line from main
public iconfig info get info if info null info new simple jdbc config info return info	get the configuration iformation for this class
public void test delete user throws exception factory delete user new sql user user1 name	test number 3
public void setup command line options options super setup command line options options add option option builder is required with description com babeldoc core i18n get sql 002 with long opt directory has arg create d	setup the options on the command line
public void test delete user preferences throws exception iuser context ctx factory get user context user1 name factory delete user preference ctx get user preference1 factory delete user preference ctx get user preference2	test number 19
public string get pipeline name return this pipeline name	get the pipeline name
public string get description return simple non pooled jdbc connection resource check in and checkouts create and destroy connections	return description of this worker
public void test get global preferences throws exception string value1 factory get global preference preference1 string value2 factory get global preference preference2 assert equals value1 user2 name assert equals value2 user1 name	test number 12
public string get name return jdbc	return the name
public void test get org preferences throws exception iorganization org factory get organization org2 name string value1 factory get organization preference org preference1 string value2 factory get organization preference org preference2 assert equals value1 org2 name assert equals value2 org1 name	test number 15
public iconfig create config string name return new default config name this	create a new iconfig based class
public void test get organization throws exception iorganization organization factory get organization org1 name assert not null organization	test number 7 test getting an organization
public void test get user preferences throws exception iuser context ctx factory get user context user1 name string value1 factory get user preference ctx get user preference1 string value2 factory get user preference ctx get user preference2 assert equals value1 org2 name assert equals value2 org1 name	test number 18
protected string buffer get tickets process query string journal query j query string buffer query super get tickets process query string j query limit stuff if j query get start index 0 query append limit j query get start index offset j query get num results hack alert need to do this to stop the parent skipping on the result set the above comment was taken from the my sql implementation i don t know how it effects postgre sql j query set start index 0 return query	get tickets process query string concoct the query string from the bits and
public ijournal ticket new ticket throws journal exception try get log debug postgre sql journal new ticket called long next val get new log id ijournal ticket ticket new journal ticket next val log the operation log ticket journal operation new ticket null null null return ticket catch exception ex throw new journal exception generic sql journal new ticket ex	get a ticket for tracking a document
public void set resolver ipipeline stage resolver resolver this resolver resolver apply the values from the pipeline data to the info options get info apply config data this get resolver get config this get name	set the resolver
public void test getting organization users throws exception iorganization parent factory get organization org2 name iuser users parent get users assert equals users length 2	test number 10
public void test set global preferences throws exception factory create global preference preference1 user2 name factory create global preference preference2 user1 name	test number 11
public void test set org preferences throws exception iorganization org factory get organization org2 name factory create organization preference org preference1 org2 name factory create organization preference org preference2 org1 name	test number 14
public void test set user preferences throws exception iuser context ctx factory get user context user1 name factory create user preference ctx get user preference1 org2 name factory create user preference ctx get user preference2 org1 name	test number 17
public ipipeline stage resolver get resolver return this resolver	get the resolver
public string get next table id string resource name string table iresource resource resource factory get resource resource name connection connection null try connection connection resource check out return table key helper get next id connection table to string catch exception e log service get instance log error e finally try resource check in connection catch exception e return null	get the next key in the database
public void test user uniqueness throws exception try test create user low level catch exception e exception good return fail exception should have been thrown	test number 2 test creating two users of same name
private void delete user resource connection connection int res id prepared statement pstmt null try pstmt connection prepare statement sql query manager get sql query res delete pstmt set int 1 res id pstmt execute update catch exception e com babeldoc core log service get instance log error exception e finally try pstmt close catch exception e	delete the resource
public void execute sql update string resource name string sql iresource resource resource factory get resource resource name connection connection null statement stmt null try connection connection resource check out stmt connection create statement stmt execute update sql catch exception e log service get instance log error e finally try stmt close catch exception e try resource check in connection catch exception e	execute sql update
protected void set up throws exception com babeldoc core environment loader load environment factory new sql user factory	set up test
protected long get next step connection con long id throws sqlexception prepared statement pstmt null result set rset null string log max step stmt sql query manager get sql query log maxstep try pstmt con prepare statement log max step stmt pstmt set long 1 id rset pstmt execute query if rset next long step rset get long 1 return step 1 else return 0 catch sqlexception se throw se finally try if rset null rset close if pstmt null pstmt close catch exception e log log error generic sql journal get next step close e	find the next available step for the log identifier
private connection get connection throws resource exception if resource null resource resource factory get resource get options resource name if resource null throw new resource exception i18n get sql 103 return connection resource check out	get the conection from the resource factory
public void remove config change listener iconfig change listener listener all listeners remove listener iterator i change listener configs key set iterator while i has next string config string i next list config list list change listener configs get config config list remove listener	remove an existing listener
public boolean has option string key string name this get options key return name null	does the configuration datastore contain this name key
public set get depends on set set new hash set set add core set add web return set	soap module only depends on web and core
public void config changed string config list config list list change listener configs get config if config list null for int i 0 i config list size i iconfig change listener l iconfig change listener config list get i l config changed new config change event config	fire a config changed event
private pipeline document create pipeline document document document output format outformat new output format 2007 11 08 paspes write xml files with selected document encoding output format outformat output format create compact format outformat set encoding this get options encoding string writer string writer new string writer xmlwriter writer new xmlwriter string writer outformat try writer write document writer flush catch ioexception e pipeline document new doc new pipeline document this get document string writer to string get bytes new doc set mime type xml mime type return new doc	create a pipeline document from the dom4 j object
public boolean has option string key string subkey string name this get options key subkey return name null	does the configuration datastore contain this name key
public void set url string url this hostport url	sets the host and port part of the soap url
public string get url return hostport	gets the host and port part of the soap url
public void run string file try get soap body to include in the soap envelope input source xml source new input source com babeldoc core resource loader get resource stream file run xml source catch exception e e print stack trace	run the soap client
protected string buffer get tickets process query string journal query j query boolean where added string buffer query new string buffer sql query manager get sql query log query tickets where added get tickets process dates j query get start date j query get end date query where added get tickets process journal operations where added query j query get journal operations get tickets process query options j query get query options query return query	get tickets process query string concoct the query string from the bits and
public void initialize set additional info	initialize the pipeline stage
private string get soap url string buffer url new string buffer http hostport ctx pipeline dot feed if attributes size 0 url append for enumeration e attributes keys e has more elements string name string e next element string value string attributes get name url append name value url append dummy dummy return url to string	get the url to send the message
private void debug header http servlet request request if log is debug enabled log log debug n received request n traverse the http headers and show them on the screen for enumeration en request get header names en has more elements string header string en next element string value request get header header if log is debug enabled log log debug header value if log is debug enabled log log debug	debug the header
public string get next stage string pipeline string stage name try string next stage pipeline factory factory get pipeline stage factory pipeline get next pipeline stage stage name return next stage null next stage catch pipeline exception pipex com babeldoc core log service get instance log error pipex return null	get the name of the next stage from this stage
public int replay ticket step journal ticket ticket int step try journal replay ticket ticket step catch exception e com babeldoc core log service get instance log error e return step	replay the ticket at the step
public string get pipeline entry stage string pipeline try ipipeline stage factory pstage factory pipeline factory factory get pipeline stage factory pipeline log service get instance log debug object pstage factory return pipeline factory factory get pipeline stage factory pipeline get entry stage name catch pipeline exception pipex log service get instance log error pipex return null	get the entry stage for the pipeline
public int step from string string sstr return integer parse int sstr	convert a string to step number
public module listing context get module listing if module listing null module listing new module listing context return module listing	get the module listing context or create one if necessary
public boolean is stage tracked string pipeline string stage name try return pipeline factory factory get pipeline stage factory pipeline is stage tracked stage name catch pipeline exception pipex com babeldoc core log service get instance log error pipex return false	get the name of the next stage from this stage
public boolean is ignored if has option ignored return true equals ignore case this get options ignored else return false	should processing document in this pipeline stage be skipped
public journal ticket ticket from string string tstr return new journal ticket long parse long tstr	convert a string to a ticket
public pipeline listing context get pipeline listing if pipeline listing null pipeline listing new pipeline listing context return pipeline listing	get the pipeline context object or create one if necessary
public string image string image return request get context path images image	load an image
public string map url string url string context request get context path log service get instance log debug url url context context if context null context starts with if url starts with log service get instance log debug resultant url context url return context url return url	convert absolutes paths to contextually correct absolute paths
public boolean is tracked if has option tracked return true equals ignore case this get options tracked else return false	must this pipeline stage track its data object
private string get mimetype string transcode str this get options transcode if transcode str equals ignore case jpeg return image jpeg else if transcode str equals ignore case png return image png else if transcode str equals ignore case tiff return image tiff else return image	get the mimetype from the destination image format
private transcoder get transcoder throws pipeline exception transcoder transcoder string transcode str this get options transcode if transcode str equals ignore case jpeg transcoder new jpegtranscoder transcoder quality transcoder transcoder width transcoder trancoder heigth transcoder else if transcode str equals ignore case png transcoder new pngtranscoder else if transcode str equals ignore case tiff transcoder new tifftranscoder else throw new pipeline exception i18n get module pipeline stage svgtranscode 7 return transcoder	get the transcoder determined by the out image type
private void trancoder heigth transcoder transcoder throws pipeline exception try transcoder add transcoding hint jpegtranscoder key height new float this get options height catch exception e throw new pipeline exception i18n get module pipeline stage svgtranscode 6 e	get the height of the output document
public iconfig info get info if info null info new sql journal info return info	get the configuraiton information object for this class
public void set module search path string module search path this module search path module search path	this is a required property
private void transcoder quality transcoder transcoder int quality 80 if this has option quality quality integer parse int this get options quality transcoder add transcoding hint jpegtranscoder key quality new float float quality 100	set the transcoder quality
public void delete global preference string key throws user exception connection connection null prepared statement pstmt null result set results null try connection connection resource check out pstmt sql query manager prepare statement connection pref gbl delete pstmt set string 1 key pstmt execute update catch exception e com babeldoc core log service get instance log error sql user factory delete global preference exception e finally try results close catch exception e try pstmt close catch exception e try connection close catch exception e	delete the global preference string for the organization
private void transcoder width transcoder transcoder throws pipeline exception try transcoder add transcoding hint jpegtranscoder key width new float this get options width catch exception e throw new pipeline exception i18n get module pipeline stage svgtranscode 5 e	set the transcoder width
public void execute throws build exception path convert pc new path convert pc set project project pc set refid path in pc set property path trimmer internal 1 pc set targetos unix pc execute pc set refid trim prefix pc set property path trimmer internal 2 pc execute string str path in project get property path trimmer internal 1 string str trim prefix project get property path trimmer internal 2 string result str path in replace all str trim prefix replace all project set new property path out result	do the work
public void set modules property string modules property this modules property modules property	this is a required property
protected iresource get resource if resource null string resource name get info get str value resource name resource resource factory get resource resource name return resource	get the resource for this journal
public void set subdirectories string subdirectories this subdirectories subdirectories	this is not a required property
public collection get type specific options collection options new array list options add new config option generic sql journal resource name iconfig option type filename null true the journal log file each operation is logged to this file return options	this method returns type specific options
public string get description return the sql journal stores its configuration information in a rdbms	return description of this worker
public string get name return sql	return the name
public void delete user iuser user throws user exception connection connection null prepared statement pstmt null try connection connection resource check out com babeldoc core log service get instance log debug delete user deleting user name user get name pstmt sql query manager prepare statement connection user delete pstmt set string 1 user get name pstmt execute update catch exception e throw new user create exception e exception deleting user finally try pstmt close catch exception e try resource check in connection catch exception e	strong delete user strong delete a user
public void set progress indeterminate boolean a status progress set indeterminate a status progress set visible a status	set the status of the messenger progressbar
public void set progress message string a string progress set string a string	set the string to be displayed in the messenger progressbar
public jprogress bar get progress bar return progress	get the progressbar used by the messenger
public void set species vector swiss prot composition a compositions super remove all elements for int i 0 i a compositions size i super add element a compositions get i	set the swiss prot compositions inside the combobox
public boolean is feasable to proceed return i feasable to proceed	returns a message why the panel was not ready to proceed
private void message object a message i messenger send message a message	send a message to the progressbar
public void pack super pack set size new dimension 1000 640	this method packs the frame
public jpanel get content pane return jpan content	this method gives the jpanel with all the content of this wizard panel
public jpanel get content return jpan content	returns the content panel of the wizzard
public void back clicked neutralize that actions that have been undertaken main information feeder get instance clear experiment sequence set experiment type enum experiment main information feeder get instance clear experiment sequence set experiment type enum experiment two txt sequence set text txt sequences two set text spin anchor set value 1 if chk second set is selected chk second set do click set feasable to proceed true	this method will be performed when the back button is clicked
private void create uicomponents image icon l icon url l url l url class loader get system resource icons back png l icon new image icon l url btn back new jbutton l icon btn back set tool tip text go one step back l url class loader get system resource icons forward png l icon new image icon l url btn forward new jbutton l icon btn forward set tool tip text go one step forward	private method to customize gui components
public void next clicked set feasable to proceed true if txt sequence get text equals ignore case set feasable to proceed false set not feasable reason your experimental set is not defined if txt sequences two get text equals ignore case chk second set is selected set feasable to proceed false set not feasable reason your experimental set is not defined	this method will be performed when the next button is clicked
public string get title string l title define the experimental set if is regional sampling l title l title and set the regional anchor return l title	returns a title for the step
protected void finalize throws throwable i timer stop super finalize	finish the timer and perform main finalization
public void action performed final action event e if chk second set is selected set sequence two visible true else set sequence two visible false	invoked when an action occurs

protected void set db name string db name this db name db name

set the db username

public void test create sub organization throws exception iorganization parent factory get organization org1 name iorganization organization factory create organization org2 name sql organization parent get id assert not null organization

test number 8

public string get options string key string subkey return templatized value return get options key subkey true

get the name of the next stage in the pipeline

protected string get db passwd if db passwd null db passwd get info get str value db passwd return db passwd

get the db password

protected void set db passwd string db passwd this db passwd db passwd

set the db password

public void test create user high level throws exception user user new sql user user2 name password user credential credential new password user credential password iuser context context factory create user user credential assert not null context factory delete user user

test number 4 creation of users using high level interface

private void release connection connection conn throws config exception try if cache connection conn close catch sqlexception e throw new config exception i18n get sql 109 e

release connection called to release the connection object

protected string get db url if db url null db url get info get str value db url return db url

get the db url

protected void set db url string db url this db url db url

set the db url

public void add resource user resource user resource throws user exception this add resource user resource iuser null

add resource add a resource

public void test create user low level throws exception iuser context context factory create user user1 name password assert not null context

test number 1 test low level user creation

protected string get db driver if db driver null db driver get info get str value db driver return db driver

get the db driver

public void test delete global preferences throws exception factory delete global preference preference1 factory delete global preference preference2

test number 13

public iconfig get config string name locale locale string country locale get country string language locale get language if country null name country if language null name language return get config name

get child a config bundle for the name and given locale

private connection get connection throws resource exception if resource null resource resource factory get resource this get options resource name if resource null throw new resource exception i18n get sql 103 return connection resource check out

get the named resource name from the resource factory

public void test delete org preferences throws exception iorganization org factory get organization org2 name factory delete organization preference org preference1 factory delete organization preference org preference2

test number 16

public void execute command line command line if command line has option d string dir command line get option value d directory new file dir if directory is directory this sql config service new sql config service process directory else system err println i18n get sql 004 dir else print usage

handle the command line from main

public iconfig info get info if info null info new simple jdbc config info return info

get the configuration iformation for this class

public void test delete user throws exception factory delete user new sql user user1 name

test number 3

public void setup command line options options super setup command line options options add option option builder is required with description com babeldoc core i18n get sql 002 with long opt directory has arg create d

setup the options on the command line

public void test delete user preferences throws exception iuser context ctx factory get user context user1 name factory delete user preference ctx get user preference1 factory delete user preference ctx get user preference2

test number 19

public string get pipeline name return this pipeline name

get the pipeline name

public string get description return simple non pooled jdbc connection resource check in and checkouts create and destroy connections

return description of this worker

public void test get global preferences throws exception string value1 factory get global preference preference1 string value2 factory get global preference preference2 assert equals value1 user2 name assert equals value2 user1 name

test number 12

public string get name return jdbc

return the name

public void test get org preferences throws exception iorganization org factory get organization org2 name string value1 factory get organization preference org preference1 string value2 factory get organization preference org preference2 assert equals value1 org2 name assert equals value2 org1 name

test number 15

public iconfig create config string name return new default config name this

create a new iconfig based class

public void test get organization throws exception iorganization organization factory get organization org1 name assert not null organization

test number 7 test getting an organization

public void test get user preferences throws exception iuser context ctx factory get user context user1 name string value1 factory get user preference ctx get user preference1 string value2 factory get user preference ctx get user preference2 assert equals value1 org2 name assert equals value2 org1 name

test number 18

protected string buffer get tickets process query string journal query j query string buffer query super get tickets process query string j query limit stuff if j query get start index 0 query append limit j query get start index offset j query get num results hack alert need to do this to stop the parent skipping on the result set the above comment was taken from the my sql implementation i don t know how it effects postgre sql j query set start index 0 return query

get tickets process query string concoct the query string from the bits and

public ijournal ticket new ticket throws journal exception try get log debug postgre sql journal new ticket called long next val get new log id ijournal ticket ticket new journal ticket next val log the operation log ticket journal operation new ticket null null null return ticket catch exception ex throw new journal exception generic sql journal new ticket ex

get a ticket for tracking a document

public void set resolver ipipeline stage resolver resolver this resolver resolver apply the values from the pipeline data to the info options get info apply config data this get resolver get config this get name

set the resolver

public void test getting organization users throws exception iorganization parent factory get organization org2 name iuser users parent get users assert equals users length 2

test number 10

public void test set global preferences throws exception factory create global preference preference1 user2 name factory create global preference preference2 user1 name

test number 11

public void test set org preferences throws exception iorganization org factory get organization org2 name factory create organization preference org preference1 org2 name factory create organization preference org preference2 org1 name

test number 14

public void test set user preferences throws exception iuser context ctx factory get user context user1 name factory create user preference ctx get user preference1 org2 name factory create user preference ctx get user preference2 org1 name

test number 17

public ipipeline stage resolver get resolver return this resolver

get the resolver

public string get next table id string resource name string table iresource resource resource factory get resource resource name connection connection null try connection connection resource check out return table key helper get next id connection table to string catch exception e log service get instance log error e finally try resource check in connection catch exception e return null

get the next key in the database

public void test user uniqueness throws exception try test create user low level catch exception e exception good return fail exception should have been thrown

test number 2 test creating two users of same name

private void delete user resource connection connection int res id prepared statement pstmt null try pstmt connection prepare statement sql query manager get sql query res delete pstmt set int 1 res id pstmt execute update catch exception e com babeldoc core log service get instance log error exception e finally try pstmt close catch exception e

delete the resource

public void execute sql update string resource name string sql iresource resource resource factory get resource resource name connection connection null statement stmt null try connection connection resource check out stmt connection create statement stmt execute update sql catch exception e log service get instance log error e finally try stmt close catch exception e try resource check in connection catch exception e

execute sql update

protected void set up throws exception com babeldoc core environment loader load environment factory new sql user factory

set up test

protected long get next step connection con long id throws sqlexception prepared statement pstmt null result set rset null string log max step stmt sql query manager get sql query log maxstep try pstmt con prepare statement log max step stmt pstmt set long 1 id rset pstmt execute query if rset next long step rset get long 1 return step 1 else return 0 catch sqlexception se throw se finally try if rset null rset close if pstmt null pstmt close catch exception e log log error generic sql journal get next step close e

find the next available step for the log identifier

private connection get connection throws resource exception if resource null resource resource factory get resource get options resource name if resource null throw new resource exception i18n get sql 103 return connection resource check out

get the conection from the resource factory

public void remove config change listener iconfig change listener listener all listeners remove listener iterator i change listener configs key set iterator while i has next string config string i next list config list list change listener configs get config config list remove listener

remove an existing listener

public boolean has option string key string name this get options key return name null

does the configuration datastore contain this name key

public set get depends on set set new hash set set add core set add web return set

soap module only depends on web and core

public void config changed string config list config list list change listener configs get config if config list null for int i 0 i config list size i iconfig change listener l iconfig change listener config list get i l config changed new config change event config

fire a config changed event

private pipeline document create pipeline document document document output format outformat new output format 2007 11 08 paspes write xml files with selected document encoding output format outformat output format create compact format outformat set encoding this get options encoding string writer string writer new string writer xmlwriter writer new xmlwriter string writer outformat try writer write document writer flush catch ioexception e pipeline document new doc new pipeline document this get document string writer to string get bytes new doc set mime type xml mime type return new doc

create a pipeline document from the dom4 j object

public boolean has option string key string subkey string name this get options key subkey return name null

does the configuration datastore contain this name key

public void set url string url this hostport url

sets the host and port part of the soap url

public string get url return hostport

gets the host and port part of the soap url

public void run string file try get soap body to include in the soap envelope input source xml source new input source com babeldoc core resource loader get resource stream file run xml source catch exception e e print stack trace

run the soap client

protected string buffer get tickets process query string journal query j query boolean where added string buffer query new string buffer sql query manager get sql query log query tickets where added get tickets process dates j query get start date j query get end date query where added get tickets process journal operations where added query j query get journal operations get tickets process query options j query get query options query return query

get tickets process query string concoct the query string from the bits and

public void initialize set additional info

initialize the pipeline stage

private string get soap url string buffer url new string buffer http hostport ctx pipeline dot feed if attributes size 0 url append for enumeration e attributes keys e has more elements string name string e next element string value string attributes get name url append name value url append dummy dummy return url to string

get the url to send the message

private void debug header http servlet request request if log is debug enabled log log debug n received request n traverse the http headers and show them on the screen for enumeration en request get header names en has more elements string header string en next element string value request get header header if log is debug enabled log log debug header value if log is debug enabled log log debug

debug the header

public string get next stage string pipeline string stage name try string next stage pipeline factory factory get pipeline stage factory pipeline get next pipeline stage stage name return next stage null next stage catch pipeline exception pipex com babeldoc core log service get instance log error pipex return null

get the name of the next stage from this stage

public int replay ticket step journal ticket ticket int step try journal replay ticket ticket step catch exception e com babeldoc core log service get instance log error e return step

replay the ticket at the step

public string get pipeline entry stage string pipeline try ipipeline stage factory pstage factory pipeline factory factory get pipeline stage factory pipeline log service get instance log debug object pstage factory return pipeline factory factory get pipeline stage factory pipeline get entry stage name catch pipeline exception pipex log service get instance log error pipex return null

get the entry stage for the pipeline

public int step from string string sstr return integer parse int sstr

convert a string to step number

public module listing context get module listing if module listing null module listing new module listing context return module listing

get the module listing context or create one if necessary

public boolean is stage tracked string pipeline string stage name try return pipeline factory factory get pipeline stage factory pipeline is stage tracked stage name catch pipeline exception pipex com babeldoc core log service get instance log error pipex return false

get the name of the next stage from this stage

public boolean is ignored if has option ignored return true equals ignore case this get options ignored else return false

should processing document in this pipeline stage be skipped

public journal ticket ticket from string string tstr return new journal ticket long parse long tstr

convert a string to a ticket

public pipeline listing context get pipeline listing if pipeline listing null pipeline listing new pipeline listing context return pipeline listing

get the pipeline context object or create one if necessary

public string image string image return request get context path images image

load an image

public string map url string url string context request get context path log service get instance log debug url url context context if context null context starts with if url starts with log service get instance log debug resultant url context url return context url return url

convert absolutes paths to contextually correct absolute paths

public boolean is tracked if has option tracked return true equals ignore case this get options tracked else return false

must this pipeline stage track its data object

private string get mimetype string transcode str this get options transcode if transcode str equals ignore case jpeg return image jpeg else if transcode str equals ignore case png return image png else if transcode str equals ignore case tiff return image tiff else return image

get the mimetype from the destination image format

private transcoder get transcoder throws pipeline exception transcoder transcoder string transcode str this get options transcode if transcode str equals ignore case jpeg transcoder new jpegtranscoder transcoder quality transcoder transcoder width transcoder trancoder heigth transcoder else if transcode str equals ignore case png transcoder new pngtranscoder else if transcode str equals ignore case tiff transcoder new tifftranscoder else throw new pipeline exception i18n get module pipeline stage svgtranscode 7 return transcoder

get the transcoder determined by the out image type

private void trancoder heigth transcoder transcoder throws pipeline exception try transcoder add transcoding hint jpegtranscoder key height new float this get options height catch exception e throw new pipeline exception i18n get module pipeline stage svgtranscode 6 e

get the height of the output document

public iconfig info get info if info null info new sql journal info return info

get the configuraiton information object for this class

public void set module search path string module search path this module search path module search path

this is a required property

private void transcoder quality transcoder transcoder int quality 80 if this has option quality quality integer parse int this get options quality transcoder add transcoding hint jpegtranscoder key quality new float float quality 100

set the transcoder quality

public void delete global preference string key throws user exception connection connection null prepared statement pstmt null result set results null try connection connection resource check out pstmt sql query manager prepare statement connection pref gbl delete pstmt set string 1 key pstmt execute update catch exception e com babeldoc core log service get instance log error sql user factory delete global preference exception e finally try results close catch exception e try pstmt close catch exception e try connection close catch exception e

delete the global preference string for the organization

private void transcoder width transcoder transcoder throws pipeline exception try transcoder add transcoding hint jpegtranscoder key width new float this get options width catch exception e throw new pipeline exception i18n get module pipeline stage svgtranscode 5 e

set the transcoder width

public void execute throws build exception path convert pc new path convert pc set project project pc set refid path in pc set property path trimmer internal 1 pc set targetos unix pc execute pc set refid trim prefix pc set property path trimmer internal 2 pc execute string str path in project get property path trimmer internal 1 string str trim prefix project get property path trimmer internal 2 string result str path in replace all str trim prefix replace all project set new property path out result

do the work

public void set modules property string modules property this modules property modules property

this is a required property

protected iresource get resource if resource null string resource name get info get str value resource name resource resource factory get resource resource name return resource

get the resource for this journal

public void set subdirectories string subdirectories this subdirectories subdirectories

this is not a required property

public collection get type specific options collection options new array list options add new config option generic sql journal resource name iconfig option type filename null true the journal log file each operation is logged to this file return options

this method returns type specific options

public string get description return the sql journal stores its configuration information in a rdbms

return description of this worker

public string get name return sql

return the name

public void delete user iuser user throws user exception connection connection null prepared statement pstmt null try connection connection resource check out com babeldoc core log service get instance log debug delete user deleting user name user get name pstmt sql query manager prepare statement connection user delete pstmt set string 1 user get name pstmt execute update catch exception e throw new user create exception e exception deleting user finally try pstmt close catch exception e try resource check in connection catch exception e

strong delete user strong delete a user

public void set progress indeterminate boolean a status progress set indeterminate a status progress set visible a status

set the status of the messenger progressbar

public void set progress message string a string progress set string a string

set the string to be displayed in the messenger progressbar

public jprogress bar get progress bar return progress

get the progressbar used by the messenger

public void set species vector swiss prot composition a compositions super remove all elements for int i 0 i a compositions size i super add element a compositions get i

set the swiss prot compositions inside the combobox

public boolean is feasable to proceed return i feasable to proceed

returns a message why the panel was not ready to proceed

private void message object a message i messenger send message a message

send a message to the progressbar

public void pack super pack set size new dimension 1000 640

this method packs the frame

public jpanel get content pane return jpan content

this method gives the jpanel with all the content of this wizard panel

public jpanel get content return jpan content

returns the content panel of the wizzard

public void back clicked neutralize that actions that have been undertaken main information feeder get instance clear experiment sequence set experiment type enum experiment main information feeder get instance clear experiment sequence set experiment type enum experiment two txt sequence set text txt sequences two set text spin anchor set value 1 if chk second set is selected chk second set do click set feasable to proceed true

this method will be performed when the back button is clicked

private void create uicomponents image icon l icon url l url l url class loader get system resource icons back png l icon new image icon l url btn back new jbutton l icon btn back set tool tip text go one step back l url class loader get system resource icons forward png l icon new image icon l url btn forward new jbutton l icon btn forward set tool tip text go one step forward

private method to customize gui components

public void next clicked set feasable to proceed true if txt sequence get text equals ignore case set feasable to proceed false set not feasable reason your experimental set is not defined if txt sequences two get text equals ignore case chk second set is selected set feasable to proceed false set not feasable reason your experimental set is not defined

this method will be performed when the next button is clicked

public string get title string l title define the experimental set if is regional sampling l title l title and set the regional anchor return l title

returns a title for the step

protected void finalize throws throwable i timer stop super finalize

finish the timer and perform main finalization

public void action performed final action event e if chk second set is selected set sequence two visible true else set sequence two visible false

invoked when an action occurs