apollo.config
Class TigrAnnotDisplayPrefs

java.lang.Object
  apollo.config.DefaultDisplayPrefs
      apollo.config.TigrAnnotDisplayPrefs

All Implemented Interfaces:

DisplayPrefsI

public class TigrAnnotDisplayPrefs
extends DefaultDisplayPrefs

Display preferences for TIGR chado annotation databases.

Version:

$Revision: 1.1 $ $Date: 2006-09-15 17:36:57 $ $Author: jcrabtree $

Nested Class Summary

protected class

TigrAnnotDisplayPrefs.TigrFeatureName Parse standard TIGR chado uniquename of the form 'eha3.assembly.1234.1' into its component parts.

Field Summary

protected static java.util.regex.Pattern	niaaGbIdPattern
protected static java.util.regex.Pattern	niaaRfIdPattern
protected static java.util.regex.Pattern	niaaSpIdPattern
protected static java.util.regex.Pattern	pfamIdPattern
protected static java.util.regex.Pattern	tigrFeatNamePattern
protected static java.util.regex.Pattern	urlDbPattern
protected static java.util.regex.Pattern	urlHitSeqNamePattern
protected static java.util.regex.Pattern	urlIdNumPattern
protected static java.util.regex.Pattern	urlIdPattern
protected static java.util.regex.Pattern	urlTypePattern
protected static java.util.regex.Pattern	urlVerPattern

Fields inherited from class apollo.config.DefaultDisplayPrefs

logger

Constructor Summary

TigrAnnotDisplayPrefs()

Method Summary

java.lang.String	generateURL(SeqFeatureI f) URLs are generated by taking the URL template ("weburl") defined in the feature file and replacing the following special strings with values extracted from the seq feature.
java.lang.String	getDisplayName(RangeI r)
protected java.lang.String	getHitSeqName(RangeI r, boolean forUrl)

Methods inherited from class apollo.config.DefaultDisplayPrefs

getBioTypeForDisplay, getHeader, getIdForURL, getPublicName, getTitle, getURLPrefix

Methods inherited from class java.lang.Object

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

Field Detail

tigrFeatNamePattern

protected static java.util.regex.Pattern tigrFeatNamePattern

urlIdPattern

protected static java.util.regex.Pattern urlIdPattern

urlDbPattern

protected static java.util.regex.Pattern urlDbPattern

urlTypePattern

protected static java.util.regex.Pattern urlTypePattern

urlIdNumPattern

protected static java.util.regex.Pattern urlIdNumPattern

urlVerPattern

protected static java.util.regex.Pattern urlVerPattern

urlHitSeqNamePattern

protected static java.util.regex.Pattern urlHitSeqNamePattern

pfamIdPattern

protected static java.util.regex.Pattern pfamIdPattern

niaaGbIdPattern

protected static java.util.regex.Pattern niaaGbIdPattern

niaaRfIdPattern

protected static java.util.regex.Pattern niaaRfIdPattern

niaaSpIdPattern

protected static java.util.regex.Pattern niaaSpIdPattern

Constructor Detail

TigrAnnotDisplayPrefs

public TigrAnnotDisplayPrefs()

Method Detail

generateURL

public java.lang.String generateURL(SeqFeatureI f)

URLs are generated by taking the URL template ("weburl") defined in the feature file and replacing the following special strings with values extracted from the seq feature. __ID__ - feature.getId() non-search hit features only (these fields are parsed from getId()): __DB__ - feature database name __TYPE__ - feature type __IDNUM__ - feature id "number" __VER__ - feature version search hit features only: __HIT_SEQ_NAME__ - name of the "hit" sequence

Specified by:

generateURL in interface DisplayPrefsI

Overrides:

generateURL in class DefaultDisplayPrefs

getDisplayName

public java.lang.String getDisplayName(RangeI r)

Specified by:

getDisplayName in interface DisplayPrefsI

Overrides:

getDisplayName in class DefaultDisplayPrefs

getHitSeqName

protected java.lang.String getHitSeqName(RangeI r,
                                         boolean forUrl)