A C D G I M O P S

A

addAlignment(Alignment) - Method in class org.vectorbase.gdav.beans.Model
 
addAnnotationTable(AnnotationTable) - Method in class org.vectorbase.gdav.beans.Model
 
addRow(AnnotationRow) - Method in class org.vectorbase.gdav.beans.AnnotationTable
 
Alignment - Class in org.vectorbase.gdav.beans
Alignment Javabean
Alignment() - Constructor for class org.vectorbase.gdav.beans.Alignment
empty constructor
Alignment(String, String, int, int, int, String, int, String) - Constructor for class org.vectorbase.gdav.beans.Alignment
pass basic-info constructor
AnnotationRow - Class in org.vectorbase.gdav.beans
Annotation Javabean
AnnotationRow() - Constructor for class org.vectorbase.gdav.beans.AnnotationRow
empty constructor
AnnotationRow(AnnotationTable) - Constructor for class org.vectorbase.gdav.beans.AnnotationRow
pass basic-info constructor
AnnotationTable - Class in org.vectorbase.gdav.beans
Annotation Javabean
AnnotationTable() - Constructor for class org.vectorbase.gdav.beans.AnnotationTable
empty constructor
AnnotationTable(List, String) - Constructor for class org.vectorbase.gdav.beans.AnnotationTable
pass basic-info constructor

C

ConfigInfo - Class in org.vectorbase.gdav
reads all relevant information from the optional (config.xml) config file stores this information and provides accessor classes for this and other information.
ConfigInfo(ServletContext) - Constructor for class org.vectorbase.gdav.ConfigInfo
search for config.xml file, parse for column / display configuration details
ConfigInfo() - Constructor for class org.vectorbase.gdav.ConfigInfo
'emergency' constructor - uses default values for webapp title and provides no column configuration
countSearchAll(String) - Method in class org.vectorbase.gdav.DBSQL.DBConnection
count results for all fulltext fields in all models

D

DBConnection - Class in org.vectorbase.gdav.DBSQL
Connection to gdav via JDBC
DBConnection(String) - Constructor for class org.vectorbase.gdav.DBSQL.DBConnection
make new connection from "host:port/dbname" string with default user /no password
DBConnection(String, String, String) - Constructor for class org.vectorbase.gdav.DBSQL.DBConnection
make new connection from "host:port/dbname" string with explicit user / password
destroy() - Method in class org.vectorbase.gdav.DisplayServlet
Deprecated.  
destroy() - Method in class org.vectorbase.gdav.GdavServlet
severs DBConnection, calls parent destroy method DBConnection
DisplayServlet - Class in org.vectorbase.gdav
Deprecated. As of release 1.0, replaced by GdavServlet
DisplayServlet() - Constructor for class org.vectorbase.gdav.DisplayServlet
Deprecated.  
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.vectorbase.gdav.DisplayServlet
Deprecated. Reads Get string from URL.
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.vectorbase.gdav.GdavServlet
handles get calls (see intro)
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.vectorbase.gdav.DisplayServlet
Deprecated. handle post calls (returns default response)
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.vectorbase.gdav.GdavServlet
handle post calls (returns default welcome page)

G

GdavServlet - Class in org.vectorbase.gdav
the main servlet, receives initial request from user, sets up connections to the DB and provides a simple search function.
GdavServlet() - Constructor for class org.vectorbase.gdav.GdavServlet
 
getAlignments() - Method in class org.vectorbase.gdav.beans.Model
returns ArrayList of Alignment objects
getAlignsForModel(int) - Method in class org.vectorbase.gdav.DBSQL.DBConnection
get all alignments in db for one model
getAllModels() - Method in class org.vectorbase.gdav.DBSQL.DBConnection
get all models in db
getAllSubs() - Method in class org.vectorbase.gdav.DBSQL.DBConnection
get all annotation submissions covered in db
getAnnoCount() - Method in class org.vectorbase.gdav.beans.AnnotationRow
 
getAnnoForModelAndSub(int, int) - Method in class org.vectorbase.gdav.DBSQL.DBConnection
get all records in db for one model and one submission
getAnnotation(String) - Method in class org.vectorbase.gdav.beans.AnnotationRow
 
getAnnotations() - Method in class org.vectorbase.gdav.beans.AnnotationRow
 
getAnnotationTables() - Method in class org.vectorbase.gdav.beans.Model
returns ArrayList of AnnotationTable objects
getChr() - Method in class org.vectorbase.gdav.beans.Alignment
 
getCigar() - Method in class org.vectorbase.gdav.beans.Alignment
 
getColClass(String) - Method in class org.vectorbase.gdav.ConfigInfo
get individual CSS class for column
getColClasses() - Method in class org.vectorbase.gdav.ConfigInfo
get Hashtable of CSS classes for cols
getColDisplay(String) - Method in class org.vectorbase.gdav.ConfigInfo
get individual display boolean for column (default true)
getColDisplays() - Method in class org.vectorbase.gdav.ConfigInfo
get Hashtable of display [true/false] values for cols
getColLink(String) - Method in class org.vectorbase.gdav.ConfigInfo
get individual link for column
getColLinks() - Method in class org.vectorbase.gdav.ConfigInfo
get Hashtable of hypertext formats for cols (http://www.website.com/urlFormat.html?id=####)
getCols() - Method in class org.vectorbase.gdav.beans.AnnotationTable
returns ArrayList of column titles (String)
getColumnClass(String) - Method in class org.vectorbase.gdav.beans.AnnotationTable
returns individual column css class
getColumnClasses() - Method in class org.vectorbase.gdav.beans.AnnotationTable
returns Hashtable of String objects for column css classes set via ConfigInfo object
getColumnDisplay(String) - Method in class org.vectorbase.gdav.beans.AnnotationTable
 
getColumnDisplays() - Method in class org.vectorbase.gdav.beans.AnnotationTable
returns Hashtable of Boolean objects, set via ConfigInfo object
getColumnLink(String) - Method in class org.vectorbase.gdav.beans.AnnotationTable
returns individual column link
getColumnLinks() - Method in class org.vectorbase.gdav.beans.AnnotationTable
returns Hashtable of String objects for column link formats, set via ConfigInfo object links should be in format: "http://host.name/?query=####" hashes will be replaced by result of ConfigInfo: getAnnotation
getDbHost() - Method in class org.vectorbase.gdav.ServletInfo
return host name for gdav DB
getDbName() - Method in class org.vectorbase.gdav.ServletInfo
return name for gdav DB
getDbPass() - Method in class org.vectorbase.gdav.ServletInfo
return password for gdav DB
getDbPort() - Method in class org.vectorbase.gdav.ServletInfo
return port for gdav DB
getDbString() - Method in class org.vectorbase.gdav.ServletInfo
return full url string (jdbc:mysql//host:port/name?user=user&pass=pass) for gdav DB
getDbUser() - Method in class org.vectorbase.gdav.ServletInfo
return user name for gdav DB
getDescription() - Method in class org.vectorbase.gdav.beans.AnnotationTable
 
getDescription() - Method in class org.vectorbase.gdav.beans.Model
 
getDescription() - Method in class org.vectorbase.gdav.beans.Submission
 
getDocumentRoot() - Method in class org.vectorbase.gdav.ConfigInfo
return root URL for website.
getDocumentRoot() - Method in class org.vectorbase.gdav.ServletInfo
return document root for gdav.xml
getEnd() - Method in class org.vectorbase.gdav.beans.Alignment
 
getFormatSeq() - Method in class org.vectorbase.gdav.beans.Model
returns seq formatted for ease of reading (10-base blocks, forced newline after 70bp)
getHost() - Method in class org.vectorbase.gdav.ServletInfo
return root URL for website.
getHSPs() - Method in class org.vectorbase.gdav.beans.Alignment
use cigar line to split alignment into constituent high-scoring pairs
getLocation() - Method in class org.vectorbase.gdav.beans.Alignment
 
getMethod() - Method in class org.vectorbase.gdav.beans.Alignment
 
getModelByID(int) - Method in class org.vectorbase.gdav.DBSQL.DBConnection
get one model in db
getModelByName(String) - Method in class org.vectorbase.gdav.DBSQL.DBConnection
get (hopefully one) model in db by name
getModelID() - Method in class org.vectorbase.gdav.beans.Model
 
getModelName() - Method in class org.vectorbase.gdav.beans.Model
 
getModelsByLocation(String, String, int, int) - Method in class org.vectorbase.gdav.DBSQL.DBConnection
get models in db that *overlap* location
getModelsByLocationSpecies(String, String, int, int, String) - Method in class org.vectorbase.gdav.DBSQL.DBConnection
get models in db that *overlap* location, for a particular model species
getModelsBySub(int) - Method in class org.vectorbase.gdav.DBSQL.DBConnection
get model by submission_id
getModelsWithNameLike(String) - Method in class org.vectorbase.gdav.DBSQL.DBConnection
get models in db matching name
getNoModels() - Method in class org.vectorbase.gdav.beans.Submission
 
getRemoteHeader() - Method in class org.vectorbase.gdav.ServletInfo
return the header HTML grabbed from a remote URL
getRows() - Method in class org.vectorbase.gdav.beans.AnnotationTable
 
getScore() - Method in class org.vectorbase.gdav.beans.Alignment
 
getSeq() - Method in class org.vectorbase.gdav.beans.Model
 
getSeqForModel(int) - Method in class org.vectorbase.gdav.DBSQL.DBConnection
get all alignments in db for one model
getSpp() - Method in class org.vectorbase.gdav.beans.Alignment
 
getSpp() - Method in class org.vectorbase.gdav.beans.Model
 
getSppLinks() - Method in class org.vectorbase.gdav.ConfigInfo
 
getStart() - Method in class org.vectorbase.gdav.beans.Alignment
 
getStrand() - Method in class org.vectorbase.gdav.beans.Alignment
 
getSubByID(int) - Method in class org.vectorbase.gdav.DBSQL.DBConnection
get all annotation submissions covered in db
getSubmissionID() - Method in class org.vectorbase.gdav.beans.Submission
 
getSubmitted() - Method in class org.vectorbase.gdav.beans.Submission
 
getSubsForModel(int) - Method in class org.vectorbase.gdav.DBSQL.DBConnection
get all submissions in db for one model
getTable() - Method in class org.vectorbase.gdav.beans.AnnotationRow
 
getTitle() - Method in class org.vectorbase.gdav.ConfigInfo
return title for website
getTitlesForSub(int) - Method in class org.vectorbase.gdav.DBSQL.DBConnection
get all records in db for one model and one submission

I

init() - Method in class org.vectorbase.gdav.DisplayServlet
Deprecated. reads in new servletInfo, creates DBconnection
init() - Method in class org.vectorbase.gdav.GdavServlet
reads in configFiles: ServletInfo (DB urls and basic config details) and ConfigInfo (column links and display configuration), creates DBConnection
prints errors, if any, to log

M

Model - Class in org.vectorbase.gdav.beans
Model Javabean
Model() - Constructor for class org.vectorbase.gdav.beans.Model
empty constructor
Model(int, String, String, String) - Constructor for class org.vectorbase.gdav.beans.Model
pass basic-info constructor

O

org.vectorbase.gdav - package org.vectorbase.gdav
 
org.vectorbase.gdav.beans - package org.vectorbase.gdav.beans
 
org.vectorbase.gdav.DBSQL - package org.vectorbase.gdav.DBSQL
 

P

ping() - Method in class org.vectorbase.gdav.DBSQL.DBConnection
check if DBconnection has been closed by MySQL server, throw SQLException if closed

S

searchAll(String) - Method in class org.vectorbase.gdav.DBSQL.DBConnection
search all fulltext fields in all models
ServletInfo - Class in org.vectorbase.gdav
reads all relevant information from the compulsory (gdav.xml) config file stores this information and provides accessor classes for this and other information.
ServletInfo(ServletContext) - Constructor for class org.vectorbase.gdav.ServletInfo
constructor - requires servlet context to retrieve config file
ServletInfo(InputSource) - Constructor for class org.vectorbase.gdav.ServletInfo
constructor - requires InputSource of config file
setAnnotation(String, String) - Method in class org.vectorbase.gdav.beans.AnnotationRow
 
setChr(String) - Method in class org.vectorbase.gdav.beans.Alignment
 
setCigar(String) - Method in class org.vectorbase.gdav.beans.Alignment
 
setCols(List) - Method in class org.vectorbase.gdav.beans.AnnotationTable
 
setColumnClass(String, String) - Method in class org.vectorbase.gdav.beans.AnnotationTable
 
setColumnDisplay(String, Boolean) - Method in class org.vectorbase.gdav.beans.AnnotationTable
 
setColumnLink(String, String) - Method in class org.vectorbase.gdav.beans.AnnotationTable
 
setDescription(String) - Method in class org.vectorbase.gdav.beans.AnnotationTable
 
setDescription(String) - Method in class org.vectorbase.gdav.beans.Model
 
setDescription(String) - Method in class org.vectorbase.gdav.beans.Submission
 
setEnd(int) - Method in class org.vectorbase.gdav.beans.Alignment
 
setMethod(String) - Method in class org.vectorbase.gdav.beans.Alignment
 
setModelID(int) - Method in class org.vectorbase.gdav.beans.Model
 
setModelName(String) - Method in class org.vectorbase.gdav.beans.Model
 
setNoModels(int) - Method in class org.vectorbase.gdav.beans.Submission
 
setScore(int) - Method in class org.vectorbase.gdav.beans.Alignment
 
setSeq(String) - Method in class org.vectorbase.gdav.beans.Model
 
setSpp(String) - Method in class org.vectorbase.gdav.beans.Alignment
 
setSpp(String) - Method in class org.vectorbase.gdav.beans.Model
 
setStart(int) - Method in class org.vectorbase.gdav.beans.Alignment
 
setStrand(int) - Method in class org.vectorbase.gdav.beans.Alignment
 
setSubmissionID(int) - Method in class org.vectorbase.gdav.beans.Submission
 
setSubmitted(String) - Method in class org.vectorbase.gdav.beans.Submission
 
setTable(AnnotationTable) - Method in class org.vectorbase.gdav.beans.AnnotationRow
 
severConnection() - Method in class org.vectorbase.gdav.DBSQL.DBConnection
forcibly close JDBC connection
Submission - Class in org.vectorbase.gdav.beans
Submission Javabean
Submission() - Constructor for class org.vectorbase.gdav.beans.Submission
empty constructor
Submission(int, String, String) - Constructor for class org.vectorbase.gdav.beans.Submission
pass basic-info constructor

A C D G I M O P S