Package net.sf.basedb.clients.web.servlet

Class PlotServlet

java.lang.Object

javax.servlet.GenericServlet

javax.servlet.http.HttpServlet

net.sf.basedb.clients.web.servlet.PlotServlet

All Implemented Interfaces:

Serializable, Servlet, ServletConfig

public final class PlotServlet
extends HttpServlet

This servlet can plot spot data for a bioassay or bioassay set. It uses the JFreePlot package to generate the plots. It accepts the following parameters:

Plot parameters

Parameter	Required	Default value	Description
ID	yes		The SessionControl ID. See Application.getSessionControl(String, String, String, boolean).
bioassayset_id	no		The ID of the bioassay set to plot. If no value is specified the bioassay_id is required.
bioassay_id	if a bioassay set hasn't been specified		The ID of the bioassay to plot.
type	no	scatter	The type of plot to create. Supported values are "scatter", "histogram" or "cfplot".
download	no	false	A boolean value. If 1 or true, the browser will ask to save the image on the local disk.
saveAs	no		If specified, the image is saved as a file in the BASE file structure.
overwrite	no	false	A boolean values, that is used with the "saveAs" parameter. If 1 or true, an existing file will be overwritten with the image.
width	no	600	The width of the generated image in pixels. Must be between 100 and 1000 pixels. The default and max width can be configured in the web.xml file.
height	no	400	The hieght of the generated image in pixels. Must be between 100 and 800. The default and max height can be configured in the web.xml file.
format	no	png	The format of the image, "png" and "jpg" are the only supported values.
xLog	no	false	A boolean parameter. If 1 or true the logarithm of the x values is calculated before plotting them.
yLog	no	false	A boolean parameter. If 1 or true the logarithm of the y values is calculated before plotting them.
x	yes, unless type is "cfplot"		The expression to plot on the x axis. Multiple x parameters may be specified to plot multiple series.
y	no, unless type is "scatter"		The expression to plot on the y axis. Multiple y parameters may be specified to plot multiple series.
filter	no		An optional filter expression that limits the result returned by the spot query.
title	no		The title of the plot. If not specified the plot is generated without title.
xLabel	no		The label on the x-axis. If not specified the plot is generated without label.
yLabel	no		The label on the y-axis. If not specified the plot is generated without label.
annotation	no		Can only be used when plotting a bioassay set. The only allowed value so far is "bioassay" which plots the spots for each bioassay in different series and color.
binSize	no	1.0	Only used for histogram plots. This is the range of values put into each bin in the histogram. Ie. if the size is 1, the first bin may have values from -5 to -4, the second bin from -4 to -3, and so on.
yAggregate	no	count	Only used for histogram plots. Determines what to plot on the y axis. Allowed values are "count", "mean", "sum", "max", "min", "stdev". If a value other than "count" is used an expression for the y-axis must also be specified.
hiloAggregate	no		Only used for histogram plots when the yAggregate parameter isn't "count". Allowed values are "hilomaxmin" and "hilostdev". This options adds a high-low bar to each bin that is either the max/min range or the plotted value +/- 1 standard deviation of the values in each bin.

Version:

2.0

Author:

Nicklas

See Also:

• Serialized Form

Last modified

$Date: 2021-06-04 12:40:45 +0200 (Fri, 04 Jun 2021) $

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
private static class	PlotServlet.CFResultIterator	Special implementation of a SqlResultIterator that combines the result from the parent and child into one virtual iterator.
private static class	PlotServlet.CFSqlResult	A single result row that is combined from the parent and child results. 1 --> parent A, 2 --> parent M, 3 --> parent M - child M

Field Summary

Fields

Modifier and Type	Field	Description
private String	cacheBase
private String	defaultFormat
private int	defaultHeight
private int	defaultWidth
private int	maxHeight
private int	maxWidth
private static final long	serialVersionUID

Constructor Summary

Constructors

Constructor	Description
PlotServlet()

Method Summary

Modifier and Type	Method	Description
void	doGet(HttpServletRequest request, HttpServletResponse response)
void	doPost(HttpServletRequest request, HttpServletResponse response)	Forwards requests to doGet(HttpServletRequest, HttpServletResponse)
private JFreeChart	generateCFPlot(BioAssay ba, String xLabel, String yLabel)	Generates a correction-factor plot, which is plotting the MA-data for the parent together with the difference in M between the parent and child.
void	init()

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, log, log

Methods inherited from class java.lang.Object

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

Field Details

serialVersionUID

private static final long serialVersionUID

See Also:

• Constant Field Values

maxWidth

private int maxWidth

maxHeight

private int maxHeight

defaultWidth

private int defaultWidth

defaultHeight

private int defaultHeight

defaultFormat

private String defaultFormat

cacheBase

private String cacheBase

Constructor Details

PlotServlet

public PlotServlet()

Method Details

init

public void init()
          throws ServletException

Overrides:

init in class GenericServlet

Throws:

ServletException

doGet

public void doGet(HttpServletRequest request,
 HttpServletResponse response)
           throws IOException,
ServletException

Overrides:

doGet in class HttpServlet

Throws:

IOException

ServletException

doPost

public void doPost(HttpServletRequest request,
 HttpServletResponse response)
            throws IOException,
ServletException

Forwards requests to doGet(HttpServletRequest, HttpServletResponse)

Overrides:

doPost in class HttpServlet

Throws:

IOException

ServletException

generateCFPlot

private JFreeChart generateCFPlot(BioAssay ba,
 String xLabel,
 String yLabel)
                           throws Exception

Generates a correction-factor plot, which is plotting the MA-data for the parent together with the difference in M between the parent and child.

Throws:

Exception