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java.lang.Object | +--uk.ac.sanger.psu.gfmerge.util.biotools.BioTools_old
Constructor Summary | |
BioTools_old()
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Method Summary | |
static MyTreeMap |
addToTreeMap(MyTreeMap tMap,
java.util.ArrayList locatableArrList)
AddToTreeMap method creates a binary tree of locateable objects sorted by their start location. |
static Sequence |
createNewSeqOfPickedGms(Sequence thisPredSeq,
java.util.ArrayList thisRegionsOfPickedGmsArr)
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static java.util.HashMap |
getCDnaScoredSpliceSiteHash_old(java.util.HashMap hashCDnaOverlappedGms)
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static java.util.HashMap |
getCDnaScoredSpliceSiteHash(java.util.ArrayList _arrListOfGMRegions,
java.util.HashMap hashCDnaOverlappedGms)
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static java.util.HashMap |
getExonOverlap(java.util.HashMap hashOfOverlappedGms)
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static java.util.HashMap |
getExonOverlapLength(java.util.HashMap thisHashExonOverlapSubLocs)
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static java.util.HashMap |
getExonOverlapSubLocs(java.util.HashMap thisHashExonOverlap)
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static java.lang.String |
getGenePredicterFromSequence(Sequence _sequence,
java.lang.String _fname)
getGenePredicterFromSequence method returns genefinder name of geneprediction if all features have the same 'method' value in the prediction file otherwise it throughs an exception. |
static java.util.HashMap |
getGmHashOfOverlappedFeat(boolean considerStrand,
java.util.ArrayList thisArrListOfGMRegions,
java.util.ArrayList thisArrListOfFeatRegions)
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static java.util.HashMap |
getGmScore(java.util.HashMap thisHashGmRegion,
java.util.HashMap thisHashExonOverlapLength,
java.util.HashMap thisHashEqualGms)
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static java.util.HashMap |
getHashOfEqualGms(java.util.ArrayList thisArrListOfGMRegions)
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static java.util.HashMap |
getLocRegionHash(java.util.ArrayList arrListOfRegions)
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static double |
getMaxACP(java.util.ArrayList thisArrListOfGMs)
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static java.util.ArrayList |
getRegionsOfPickedGms(java.util.ArrayList thisGmScoreTreeForRegionsArr)
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static java.util.ArrayList |
getSortedGmsInRegion(java.util.ArrayList thisArrListOfGMRegions,
java.util.HashMap thisHashGmScore)
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static StrandedFeature.Strand |
getStrand(Feature f)
getStrand Method which returns strand of given feature. |
static java.util.HashMap |
pickObjOnHighScoringPath(java.util.HashMap objScoreHash)
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static java.util.ArrayList |
search(MyTreeMap tMap)
Search method calculates regions of overlapping features. |
static Sequence |
Seqs2Seq(SequenceIterator sequences)
Seq2Seq method returns a sequence object when sequence iterator is given. |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
public BioTools_old()
Method Detail |
public static Sequence Seqs2Seq(SequenceIterator sequences)
Called by the main method in GFMerge.
sequences
- SequenceIterator object which may contain more than one
more than one sequence, but only the first sequence is
returned
SequenceIterator
,
Sequence
public static java.lang.String getGenePredicterFromSequence(Sequence _sequence, java.lang.String _fname)
Called by the main method in GFMerge.
_sequence
- Sequence object_fname
- filename of the prediction file which is needed for the
exception method
java.util.NoSuchElementException
- If no method entry is in file
"Exception"
- If different method values are in fileSequence
public static StrandedFeature.Strand getStrand(Feature f)
f
- Feature
Feature
,
StrandedFeature.Strand
public static MyTreeMap addToTreeMap(MyTreeMap tMap, java.util.ArrayList locatableArrList)
Called by the main method in GFMerge. Key is the start location of a LocateAble object, Value is an array of LocateAble objects with the same start location
tMap
- binary tree instanced from MyTreeMap
each key-value-pair contains the start location
of features as key and an array of
LocateAble
as value.
tree is empty when called first, new leaves will
be added.locatableArrList
- ArrayList
of LocateAble objects
MyTreeMap
,
LocateAble
public static java.util.ArrayList search(MyTreeMap tMap)
Called by the main method in GFMerge.
tMap
- binary tree instanced from MyTreeMap
each key-value-pair contains the start location
of features as key and an array of LocateAble
as value
ArrayList
of Regions which contain
themselves LocateAble objectsMyTreeMap
,
LocateAble
public static java.util.HashMap getLocRegionHash(java.util.ArrayList arrListOfRegions)
public static java.util.HashMap getGmHashOfOverlappedFeat(boolean considerStrand, java.util.ArrayList thisArrListOfGMRegions, java.util.ArrayList thisArrListOfFeatRegions)
public static java.util.HashMap getCDnaScoredSpliceSiteHash(java.util.ArrayList _arrListOfGMRegions, java.util.HashMap hashCDnaOverlappedGms)
public static java.util.HashMap getCDnaScoredSpliceSiteHash_old(java.util.HashMap hashCDnaOverlappedGms)
public static java.util.HashMap getHashOfEqualGms(java.util.ArrayList thisArrListOfGMRegions)
public static java.util.HashMap getExonOverlap(java.util.HashMap hashOfOverlappedGms)
public static java.util.HashMap getExonOverlapSubLocs(java.util.HashMap thisHashExonOverlap)
public static java.util.HashMap getExonOverlapLength(java.util.HashMap thisHashExonOverlapSubLocs)
public static java.util.HashMap getGmScore(java.util.HashMap thisHashGmRegion, java.util.HashMap thisHashExonOverlapLength, java.util.HashMap thisHashEqualGms)
public static java.util.ArrayList getSortedGmsInRegion(java.util.ArrayList thisArrListOfGMRegions, java.util.HashMap thisHashGmScore)
public static java.util.ArrayList getRegionsOfPickedGms(java.util.ArrayList thisGmScoreTreeForRegionsArr)
public static Sequence createNewSeqOfPickedGms(Sequence thisPredSeq, java.util.ArrayList thisRegionsOfPickedGmsArr)
public static java.util.HashMap pickObjOnHighScoringPath(java.util.HashMap objScoreHash)
public static double getMaxACP(java.util.ArrayList thisArrListOfGMs)
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