/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.bio.chromatogram;
import org.biojava.bio.symbol.IntegerAlphabet;
import org.biojava.bio.symbol.SymbolList;
/**
* Utility class for dealing with {@link Chromatogram}s.
*
* @author Rhett Sutphin (UI CBCB)
* @author Matthew Pocock
* @since 1.3
*/
public class ChromatogramTools {
/** Static utility class - don't allow it to be instantiated. */
private ChromatogramTools() { }
/**
* Get the called DNA sequence from a chromatogram. A synonym for
* chromat.getBaseCalls().symbolListForLabel(Chromatogram.DNA)
.
*
* @param chromat the Chromatogram to process
* @return a SymbolList containing the DNA
*/
public static final SymbolList getDNASequence(Chromatogram chromat) {
return chromat.getBaseCalls().symbolListForLabel(Chromatogram.DNA);
}
/**
* Get the peak offsets for the called bases of a chromatogram. A synonym
* for chromat.getBaseCalls().symbolListForLabel(Chromatogram.OFFSETS)
.
*
* @param chromat the Chromatogram to process
* @return a SymbolList of offsets
*/
public static final SymbolList getTraceOffsets(Chromatogram chromat) {
return chromat.getBaseCalls().symbolListForLabel(Chromatogram.OFFSETS);
}
/**
* Converts the peak offsets list of the given chromatogram
* into a new 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. * * @param chromat the Chromatogram to process * @return an array of integers representing peak offsets */ public static final int[] getTraceOffsetArray(Chromatogram chromat) { int[] array = new int[chromat.getSequenceLength()]; for (int i = 0 ; i < array.length ; i++) { array[i] = getTraceOffset(chromat, i+1); } return array; } /** * Get a specific value from the trace offset sequence in the given * chromatogram and extract its
int
value.
*
* @param chromat the chromatogram to examine
* @param which which symbol in the trace offset sequence to
* get. 1-based index.
* @return the offset for that peak
*/
public static final int getTraceOffset(Chromatogram chromat, int which) {
return getIntFromSymbolList(chromat.getBaseCalls().symbolListForLabel(Chromatogram.OFFSETS), which);
}
/**
* Retrieves, unwraps, and returns an int
from a
* SymbolList containing {@link org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol}s.
* @param list the target list
* @param which which symbol to unwrap and return. 1-based index.
* @return the integer represented by the symbol at that position
*/
public static final int getIntFromSymbolList(SymbolList list, int which) {
return ((IntegerAlphabet.IntegerSymbol) list.symbolAt(which)).intValue();
}
}