Package org.biojava.bio.chromatogram
Class ChromatogramTools
java.lang.Object
org.biojava.bio.chromatogram.ChromatogramTools
Utility class for dealing with
Chromatogram
s.- Since:
- 1.3
- Author:
- Rhett Sutphin (UI CBCB), Matthew Pocock
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Method Summary
Modifier and TypeMethodDescriptionstatic final SymbolList
getDNASequence
(Chromatogram chromat) Get the called DNA sequence from a chromatogram.static final int
getIntFromSymbolList
(SymbolList list, int which) Retrieves, unwraps, and returns anint
from a SymbolList containingIntegerAlphabet.IntegerSymbol
s.static final int
getTraceOffset
(Chromatogram chromat, int which) Get a specific value from the trace offset sequence in the given chromatogram and extract itsint
value.static final int[]
getTraceOffsetArray
(Chromatogram chromat) Converts the peak offsets list of the given chromatogram into a newint
array.static final SymbolList
getTraceOffsets
(Chromatogram chromat) Get the peak offsets for the called bases of a chromatogram.
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Method Details
-
getDNASequence
Get the called DNA sequence from a chromatogram. A synonym forchromat.getBaseCalls().symbolListForLabel(Chromatogram.DNA)
.- Parameters:
chromat
- the Chromatogram to process- Returns:
- a SymbolList containing the DNA
-
getTraceOffsets
Get the peak offsets for the called bases of a chromatogram. A synonym forchromat.getBaseCalls().symbolListForLabel(Chromatogram.OFFSETS)
.- Parameters:
chromat
- the Chromatogram to process- Returns:
- a SymbolList of offsets
-
getTraceOffsetArray
Converts the peak offsets list of the given chromatogram into a newint
array.The array is, of course, allocated and initialized at each call, so using this method like this:
for (int i = m ; i invalid input: '<' n ; i++) doSomething(getTraceOffsetArray(c)[i]);
is not recommended.- Parameters:
chromat
- the Chromatogram to process- Returns:
- an array of integers representing peak offsets
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getTraceOffset
Get a specific value from the trace offset sequence in the given chromatogram and extract itsint
value.- Parameters:
chromat
- the chromatogram to examinewhich
- which symbol in the trace offset sequence to get. 1-based index.- Returns:
- the offset for that peak
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getIntFromSymbolList
Retrieves, unwraps, and returns anint
from a SymbolList containingIntegerAlphabet.IntegerSymbol
s.- Parameters:
list
- the target listwhich
- which symbol to unwrap and return. 1-based index.- Returns:
- the integer represented by the symbol at that position
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