apollo.config
Class FlyDisplayPrefs

java.lang.Object
  apollo.config.DefaultDisplayPrefs
      apollo.config.FlyDisplayPrefs

All Implemented Interfaces:

DisplayPrefsI

public class FlyDisplayPrefs
extends DefaultDisplayPrefs

Field Summary

Fields inherited from class apollo.config.DefaultDisplayPrefs

logger

Constructor Summary

FlyDisplayPrefs()

Method Summary

protected java.lang.String	generateAnnotURL(AnnotatedFeatureI g, java.lang.String baseAnnotURL) For annotations, try to find the appropriate identifier to add to the base URL.
java.lang.String	generateURL(SeqFeatureI f)
java.lang.String	getBioTypeForDisplay(SeqFeatureI sf) This just returns sf.getBioType() (capitalized) unless its a transcript.
java.lang.String	getDisplayName(RangeI sf) This is used for making (short) labels in the display.
java.lang.String	getHeader(RangeI sf)
protected java.lang.String	getIdForURL(SeqFeatureI f)
java.lang.String	getTitle(CurationSet curation) generate a title for this curation
protected java.lang.String	getURLPrefix(FeatureProperty prop, SeqFeatureI f, java.lang.String id)

Methods inherited from class apollo.config.DefaultDisplayPrefs

getPublicName

Methods inherited from class java.lang.Object

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

Constructor Detail

FlyDisplayPrefs

public FlyDisplayPrefs()

Method Detail

getDisplayName

public java.lang.String getDisplayName(RangeI sf)

This is used for making (short) labels in the display.

Specified by:

getDisplayName in interface DisplayPrefsI

Overrides:

getDisplayName in class DefaultDisplayPrefs

getHeader

public java.lang.String getHeader(RangeI sf)

Specified by:

getHeader in interface DisplayPrefsI

Overrides:

getHeader in class DefaultDisplayPrefs

generateURL

public java.lang.String generateURL(SeqFeatureI f)

Specified by:

generateURL in interface DisplayPrefsI

Overrides:

generateURL in class DefaultDisplayPrefs

getIdForURL

protected java.lang.String getIdForURL(SeqFeatureI f)

Overrides:

getIdForURL in class DefaultDisplayPrefs

getURLPrefix

protected java.lang.String getURLPrefix(FeatureProperty prop,
                                        SeqFeatureI f,
                                        java.lang.String id)

Overrides:

getURLPrefix in class DefaultDisplayPrefs

generateAnnotURL

protected java.lang.String generateAnnotURL(AnnotatedFeatureI g,
                                            java.lang.String baseAnnotURL)

For annotations, try to find the appropriate identifier to add to the base URL.

getTitle

public java.lang.String getTitle(CurationSet curation)

Description copied from interface: DisplayPrefsI

generate a title for this curation

Specified by:

getTitle in interface DisplayPrefsI

Overrides:

getTitle in class DefaultDisplayPrefs

getBioTypeForDisplay

public java.lang.String getBioTypeForDisplay(SeqFeatureI sf)

This just returns sf.getBioType() (capitalized) unless its a transcript. For transcript it only returns "Transcript" if its part of a Gene. Otherwise it returns its parent's bio type + transcript. (should it not tack on the transcript?) Thus a tRNA's transcript would display "tRNA transcript", where a gene's transcript would display just "Transcript". Should it actually display "Gene transcript"? rename getTypeForDisplay?

Specified by:

getBioTypeForDisplay in interface DisplayPrefsI

Overrides:

getBioTypeForDisplay in class DefaultDisplayPrefs