|
|||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectorg.biojava.bio.chromatogram.ChromatogramTools
Utility class for dealing with Chromatogram
s.
Method Summary | |
static SymbolList |
getDNASequence(Chromatogram chromat)
Get the called DNA sequence from a chromatogram. |
static int |
getIntFromSymbolList(SymbolList list,
int which)
Retrieves, unwraps, and returns an int from a
SymbolList containing IntegerAlphabet.IntegerSymbol s. |
static int |
getTraceOffset(Chromatogram chromat,
int which)
Get a specific value from the trace offset sequence in the given chromatogram and extract its int value. |
static int[] |
getTraceOffsetArray(Chromatogram chromat)
Converts the peak offsets list of the given chromatogram into a new int array. |
static SymbolList |
getTraceOffsets(Chromatogram chromat)
Get the peak offsets for the called bases of a chromatogram. |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Method Detail |
public static final SymbolList getDNASequence(Chromatogram chromat)
chromat.getBaseCalls().symbolListForLabel(Chromatogram.DNA)
.
public static final SymbolList getTraceOffsets(Chromatogram chromat)
chromat.getBaseCalls().symbolListForLabel(Chromatogram.OFFSETS)
.
public static final int[] getTraceOffsetArray(Chromatogram chromat)
int
array.
The array is, of course, allocated and initialized at each call, so using this method like this:
for (int i = m ; i < n ; i++) doSomething(getTraceOffsetArray(c)[i]);is not recommended.
public static final int getTraceOffset(Chromatogram chromat, int which)
int
value.
chromat
- the chromatogram to examinewhich
- which symbol in the trace offset sequence to
get. 1-based index.public static final int getIntFromSymbolList(SymbolList list, int which)
int
from a
SymbolList containing IntegerAlphabet.IntegerSymbol
s.
list
- the target listwhich
- which symbol to unwrap and return. 1-based index.
|
|||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |