edu.mssm.crover.webapps.dimlib.lw
Class AlignmentViewer

java.lang.Object
  |
  +--cuttingedge.lw.form.Widget
        |
        +--cuttingedge.lw.form.Form
              |
              +--edu.mssm.crover.webapps.dimlib.lw.DiMLibForm
                    |
                    +--edu.mssm.crover.webapps.dimlib.lw.AlignmentViewer

All Implemented Interfaces:

java.io.Serializable, cuttingedge.lw.form.Visitee

public class AlignmentViewer

extends DiMLibForm

See Also:

Serialized Form

Field Summary

protected javax.jdo.PersistenceManager

pm

Fields inherited from class edu.mssm.crover.webapps.dimlib.lw.DiMLibForm

session

Fields inherited from class cuttingedge.lw.form.Widget

NAME_SEPARATOR

Constructor Summary

AlignmentViewer(cuttingedge.lw.ServletSession session)

AlignmentViewer(cuttingedge.lw.ServletSession session, boolean confirmed, int num_res, java.lang.String size)

AlignmentViewer(cuttingedge.lw.ServletSession session, boolean confirmed, int num_res, java.lang.String size, java.lang.String style, boolean links)

AlignmentViewer(cuttingedge.lw.ServletSession session, int num_res, java.lang.String size)

AlignmentViewer(cuttingedge.lw.ServletSession session, java.lang.String[] sqs)

AlignmentViewer(cuttingedge.lw.ServletSession session, java.lang.String[] sqs, boolean hd)

Method Summary

void	addSubSelection(int i)
boolean	getConfirmed()
boolean	getUseDSI()
void	setConfirmed(boolean confirmed)
void	setUseDSI(boolean useDSI)

Methods inherited from class edu.mssm.crover.webapps.dimlib.lw.DiMLibForm

assertLog, debug, debug, error, error, exit, getAllowedDatabases, getAllowedOrganismList, getAllowedOrganisms, getPersistenceManager, info, log, viewHelp, viewHelp, viewXML, warn

Methods inherited from class cuttingedge.lw.form.Form

accept, add, getByName, getChildren, getFormManager, remove, removeAll, removeByName, show

Methods inherited from class cuttingedge.lw.form.Widget

getCategory, getFullName, getLabel, getName, getParent, getProperties, getProperty, hasProperties, setCategory, setLabel, setName, setProperty

Methods inherited from class java.lang.Object

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

Field Detail

pm

protected javax.jdo.PersistenceManager pm

Constructor Detail

AlignmentViewer

public AlignmentViewer(cuttingedge.lw.ServletSession session,
                       java.lang.String[] sqs,
                       boolean hd)

AlignmentViewer

public AlignmentViewer(cuttingedge.lw.ServletSession session,
                       java.lang.String[] sqs)

AlignmentViewer

public AlignmentViewer(cuttingedge.lw.ServletSession session)

AlignmentViewer

public AlignmentViewer(cuttingedge.lw.ServletSession session,
                       int num_res,
                       java.lang.String size)

AlignmentViewer

public AlignmentViewer(cuttingedge.lw.ServletSession session,
                       boolean confirmed,
                       int num_res,
                       java.lang.String size)

AlignmentViewer

public AlignmentViewer(cuttingedge.lw.ServletSession session,
                       boolean confirmed,
                       int num_res,
                       java.lang.String size,
                       java.lang.String style,
                       boolean links)

Parameters:

num_res - number of residues to display per line

size - font size of residues (large -> small)

style - font style of residues (plain, bold, svg)

links - whether links should be displayed or not

Method Detail

addSubSelection

public void addSubSelection(int i)

getConfirmed

public boolean getConfirmed()

setConfirmed

public void setConfirmed(boolean confirmed)

getUseDSI

public boolean getUseDSI()

setUseDSI

public void setUseDSI(boolean useDSI)