uk.ac.sanger.psu.gfmerge.analysis.tools
Class HighScoringPath
java.lang.Object
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+--uk.ac.sanger.psu.gfmerge.analysis.tools.HighScoringPath
- public class HighScoringPath
- extends java.lang.Object
Method Summary |
private static java.util.HashMap |
calcHighScoringPath(java.util.HashMap clusteredObjScoreHash,
boolean isAverage)
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private static java.util.TreeMap |
getAllPaths(java.util.TreeMap allPathList,
java.util.ArrayList singlePathArr,
java.util.HashMap objScoreHash,
boolean isAverage)
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static java.util.HashMap |
getHighScoringPath(java.util.HashMap nonClusteredObjScoreHash,
java.util.ArrayList arrListOfGmRegions,
boolean isAverage)
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private static java.util.ArrayList |
getNonOverlappingObjs(java.util.ArrayList singlePathArr,
java.util.HashMap objScoreHash)
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private static double |
getPathScore(java.util.ArrayList pathArr,
java.util.HashMap objScoreHash,
boolean isAverage)
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private static boolean |
isNonOverlappingDownstreamObjFurtherUpstream(java.util.ArrayList singlePathArr)
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private static boolean |
isNonOverlappingObjUpstream(java.util.ArrayList singlePathArr,
java.util.ArrayList arrOfNonOverlappingObjs)
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static java.util.ArrayList |
removeLowScoreGmsFromRegArr(java.util.ArrayList _arrListOfGMRegions,
java.util.HashMap highScorePathGms)
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Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
HighScoringPath
public HighScoringPath()
getHighScoringPath
public static java.util.HashMap getHighScoringPath(java.util.HashMap nonClusteredObjScoreHash,
java.util.ArrayList arrListOfGmRegions,
boolean isAverage)
calcHighScoringPath
private static java.util.HashMap calcHighScoringPath(java.util.HashMap clusteredObjScoreHash,
boolean isAverage)
getAllPaths
private static java.util.TreeMap getAllPaths(java.util.TreeMap allPathList,
java.util.ArrayList singlePathArr,
java.util.HashMap objScoreHash,
boolean isAverage)
getPathScore
private static double getPathScore(java.util.ArrayList pathArr,
java.util.HashMap objScoreHash,
boolean isAverage)
getNonOverlappingObjs
private static java.util.ArrayList getNonOverlappingObjs(java.util.ArrayList singlePathArr,
java.util.HashMap objScoreHash)
isNonOverlappingObjUpstream
private static boolean isNonOverlappingObjUpstream(java.util.ArrayList singlePathArr,
java.util.ArrayList arrOfNonOverlappingObjs)
isNonOverlappingDownstreamObjFurtherUpstream
private static boolean isNonOverlappingDownstreamObjFurtherUpstream(java.util.ArrayList singlePathArr)
removeLowScoreGmsFromRegArr
public static java.util.ArrayList removeLowScoreGmsFromRegArr(java.util.ArrayList _arrListOfGMRegions,
java.util.HashMap highScorePathGms)