apollo.gui.genomemap
Class Sites

java.lang.Object
  apollo.gui.genomemap.Sites

public class Sites
extends java.lang.Object

Sites holds an array of integers which are the base positions for each site in a given frame and strand. Nothing about vertical placement is stored here. The positions are ordered in the order that they are added (addSite). Currently SiteView._createSites adds forward strand sites in ascending order, reverse strand sites in desceding order. No state as to whether start or stops stored here. That's in SiteView.

Field Summary

protected static org.apache.log4j.Logger

logger

Constructor Summary

Sites()

Method Summary

void	addSite(int pos)
void	clearSelected()
void	clearSites()
int	elementAt(int ind)
SiteCodon	getSiteCodon(int low, int high, java.lang.String type, int strand, java.lang.String namePrefix) low is not start.
SiteCodon	getSiteCodon(SeqFeatureI sf)
SiteCodon	getSiteCodon(java.lang.String name)
void	selectSite(int pos, boolean state) int of site to mark selected Presently there is no checking if pos actually exists as a site should there be? SiteView.handleFeatSel calls selectSite without knowing if site exists.
int	size()

Methods inherited from class java.lang.Object

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

Field Detail

logger

protected static final org.apache.log4j.Logger logger

Constructor Detail

Sites

public Sites()

Method Detail

addSite

public void addSite(int pos)

size

public int size()

elementAt

public int elementAt(int ind)

clearSites

public void clearSites()

selectSite

public void selectSite(int pos,
                       boolean state)

int of site to mark selected Presently there is no checking if pos actually exists as a site should there be? SiteView.handleFeatSel calls selectSite without knowing if site exists. Should it check or should Sites check? separate method with checking?

clearSelected

public void clearSelected()

getSiteCodon

public SiteCodon getSiteCodon(SeqFeatureI sf)

getSiteCodon

public SiteCodon getSiteCodon(java.lang.String name)

getSiteCodon

public SiteCodon getSiteCodon(int low,
                              int high,
                              java.lang.String type,
                              int strand,
                              java.lang.String namePrefix)

low is not start. low is absolute low. low is lower than low on both strands