org.utgenome.gwt.utgb.server.app
Class ReadView

java.lang.Object
  javax.servlet.GenericServlet
      javax.servlet.http.HttpServlet
          org.utgenome.gwt.utgb.server.RequestHandlerBase
              org.utgenome.gwt.utgb.server.WebTrackBase
                  org.utgenome.gwt.utgb.server.app.ReadView

All Implemented Interfaces:

Serializable, javax.servlet.Servlet, javax.servlet.ServletConfig, RequestHandler

public class ReadView
extends WebTrackBase

Web action for querying data in a specified window in a genome

See Also:

Serialized Form

Field Summary

String	chr
int	end
ReadQueryConfig.Layout	layout
String	path
String	ref
String	species
int	start
boolean	useCanvas
int	width

Constructor Summary

ReadView()

Method Summary

static ReadCoverage	computeCoverage(List<GenomeRange> readList, int start, int end, int pixelWidth)
void	handle(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response) Handles the HTTP request
static boolean	isDescendant(String targetPath)
static List<GenomeRange>	overlapQuery(File baseDir, GenomeDB db, ChrLoc loc, ReadQueryConfig config)
static List<GenomeRange>	overlapQuery(GenomeDB db, ChrLoc loc, ReadQueryConfig config)

Methods inherited from class org.utgenome.gwt.utgb.server.WebTrackBase

createSQL, createSQLFromFile, createSQLStatement, getActionPrefix, getActionSuffix, getDatabaseAccess, getHTTPRequestQueryString, getProjectRootPath, getTrackConfigProperty, loadJSON, loadJSON, openAction, openAction, toJSON

Methods inherited from class org.utgenome.gwt.utgb.server.RequestHandlerBase

doGet, doPost, validate

Methods inherited from class javax.servlet.http.HttpServlet

doDelete, doHead, doOptions, doPut, doTrace, getLastModified, service, service

Methods inherited from class javax.servlet.GenericServlet

destroy, getInitParameter, getInitParameterNames, getServletConfig, getServletContext, getServletInfo, getServletName, init, init, log, log

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

start

public int start

end

public int end

species

public String species

ref

public String ref

chr

public String chr

width

public int width

useCanvas

public boolean useCanvas

layout

public ReadQueryConfig.Layout layout

path

public String path

Constructor Detail

ReadView

public ReadView()

Method Detail

isDescendant

public static boolean isDescendant(String targetPath)

handle

public void handle(javax.servlet.http.HttpServletRequest request,
                   javax.servlet.http.HttpServletResponse response)
            throws javax.servlet.ServletException,
                   IOException

Description copied from interface: RequestHandler

Handles the HTTP request

Specified by:

handle in interface RequestHandler

Specified by:

handle in class RequestHandlerBase

Parameters:

request - the http servlet request

response - the http servlet response

Throws:

javax.servlet.ServletException

IOException

overlapQuery

public static List<GenomeRange> overlapQuery(GenomeDB db,
                                             ChrLoc loc,
                                             ReadQueryConfig config)

overlapQuery

public static List<GenomeRange> overlapQuery(File baseDir,
                                             GenomeDB db,
                                             ChrLoc loc,
                                             ReadQueryConfig config)

computeCoverage

public static ReadCoverage computeCoverage(List<GenomeRange> readList,
                                           int start,
                                           int end,
                                           int pixelWidth)