selex
Class SeqRead

java.lang.Object
  extended byselex.SeqRead

public class SeqRead
extends java.lang.Object

Container for information related to a particular sequencing read.


Constructor Summary
SeqRead(java.lang.String sequence, java.lang.String seqComment, java.lang.String quality, java.lang.String qualComment, SelexParams aSP, SeqFiles aSF)
           
 
Method Summary
 boolean checkEstimateNumSubSeqs()
           
static boolean checkSeqQuality(int[] qualityScores, int minNumHighQualBases, int minQualScore)
          Examines an int[] for a continuous stretch of scores
 int[][] extractSegs(java.util.ArrayList ends)
           
 java.util.ArrayList findEnds()
           
static int getNumStretchesGoodQuality(int[] qualityScores, int qualCutOff, int seqLength)
          Counts the number of stretches of scores above a cut off in an int[].
 boolean makeSubSeqs()
           
 void printSeqRead()
           
 java.util.ArrayList removeLowQualitySegs(int[][] segs)
           
 java.util.ArrayList removeOddSizedSegs(java.util.ArrayList segs)
           
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

SeqRead

public SeqRead(java.lang.String sequence,
               java.lang.String seqComment,
               java.lang.String quality,
               java.lang.String qualComment,
               SelexParams aSP,
               SeqFiles aSF)
Method Detail

checkEstimateNumSubSeqs

public boolean checkEstimateNumSubSeqs()

printSeqRead

public void printSeqRead()

makeSubSeqs

public boolean makeSubSeqs()

findEnds

public java.util.ArrayList findEnds()

extractSegs

public int[][] extractSegs(java.util.ArrayList ends)

removeLowQualitySegs

public java.util.ArrayList removeLowQualitySegs(int[][] segs)

removeOddSizedSegs

public java.util.ArrayList removeOddSizedSegs(java.util.ArrayList segs)

checkSeqQuality

public static boolean checkSeqQuality(int[] qualityScores,
                                      int minNumHighQualBases,
                                      int minQualScore)
Examines an int[] for a continuous stretch of scores


getNumStretchesGoodQuality

public static int getNumStretchesGoodQuality(int[] qualityScores,
                                             int qualCutOff,
                                             int seqLength)
Counts the number of stretches of scores above a cut off in an int[]. Useful for estimating the number of concatinated selex oligos that should be found in a sequence read