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

java.lang.Object
  extended by javax.servlet.GenericServlet
      extended by javax.servlet.http.HttpServlet
          extended by org.utgenome.gwt.utgb.server.RequestHandlerBase
              extended by org.utgenome.gwt.utgb.server.WebTrackBase
                  extended by 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)


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