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ModifiedAminoAcidCompoundSet.java
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ModifiedAminoAcidCompoundSet.java
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/*
* 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.nbio.aaproperties.xml;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
import org.biojava.nbio.core.sequence.template.CompoundSet;
import org.biojava.nbio.core.sequence.template.Sequence;
import java.util.*;
public class ModifiedAminoAcidCompoundSet implements CompoundSet<AminoAcidCompound> {
private final Map<String, AminoAcidCompound> aminoAcidCompoundCache = new HashMap<>();
public ModifiedAminoAcidCompoundSet(List<AminoAcidComposition> aaList, Map<Character, Double> aaSymbol2MolecularWeight) {
this.aminoAcidCompoundCache.put("-", new AminoAcidCompound(null, "-", "", "", 0.0f));
for (AminoAcidComposition aa : aaList) {
this.aminoAcidCompoundCache.put(aa.getSymbol(),
new AminoAcidCompound(null, aa.getSymbol(), aa.getShorName(), aa.getName(),
aaSymbol2MolecularWeight.get(aa.getSymbol().charAt(0)).floatValue()));
}
}
@Override
public int getMaxSingleCompoundStringLength() {
return 1;
}
@Override
public boolean isCompoundStringLengthEqual() {
return true;
}
@Override
public AminoAcidCompound getCompoundForString(String string) {
if (string.length() == 0) {
return null;
}
if (string.length() > this.getMaxSingleCompoundStringLength()) {
throw new IllegalArgumentException("String supplied (" + string + ") is too long. Max is " + getMaxSingleCompoundStringLength());
}
return this.aminoAcidCompoundCache.get(string);
}
@Override
public String getStringForCompound(AminoAcidCompound compound) {
return compound.toString();
}
@Override
public boolean compoundsEquivalent(AminoAcidCompound compoundOne, AminoAcidCompound compoundTwo) {
// TODO Auto-generated method stub
return false;
}
@Override
public Set<AminoAcidCompound> getEquivalentCompounds(AminoAcidCompound compound) {
// TODO Auto-generated method stub
return null;
}
@Override
public boolean hasCompound(AminoAcidCompound compound) {
return aminoAcidCompoundCache.containsValue(compound);
}
@Override
public List<AminoAcidCompound> getAllCompounds() {
return new ArrayList<>(aminoAcidCompoundCache.values());
}
@Override
public boolean isComplementable() {
return false;
}
@Override
public boolean isValidSequence(Sequence<AminoAcidCompound> sequence) {
for (AminoAcidCompound c : sequence) {
if (!hasCompound(c)) {
return false;
}
}
return true;
}
}