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TaxonNameMap.java
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TaxonNameMap.java
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package phylonet.coalescent;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import phylonet.tree.model.Tree;
import phylonet.tree.util.Trees;
/**
* Maps gene names to species names (as strings)
*
* @author smirarab
*
*/
public class TaxonNameMap {
private Map<String, String> taxonMap = null;
private String pattern = null;
private String rep = null;
private SpeciesMapper speciesIdMapper;
//Map<String, BitSet> speciesBitSet = null;
public TaxonNameMap (Map<String, String> taxonMap) {
this.taxonMap = taxonMap;
this.initializeSpeciesMapper();
}
public TaxonNameMap (String pattern, String rep) {
this.pattern = pattern;
this.rep = rep;
throw new RuntimeException("Not implemented yet");
}
public TaxonNameMap () {
this.initializeSpeciesMapper();
}
public void initializeSpeciesMapper() {
speciesIdMapper = new SpeciesMapper(GlobalMaps.taxonIdentifier.taxonCount());
if (this.taxonMap != null) {
for (Entry<String, String> entry: this.taxonMap.entrySet()) {
speciesIdMapper.setSpeciesIdForTaxon(entry.getKey(), entry.getValue());
}
} else {
for (int i = 0; i < GlobalMaps.taxonIdentifier.taxonCount(); i++) {
speciesIdMapper.setSpeciesIdForTaxon(i,GlobalMaps.taxonIdentifier.getTaxonName(i));
}
}
}
/**
* For a given gene name, give the species name
* @param geneName
* @return
*/
public String getTaxonName(String geneName) {
if (geneName == null || "".equals(geneName)) {
throw new RuntimeException("Empty name?");
}
if (this.pattern != null) {
String s = geneName.replaceAll(pattern,rep);
//System.err.println("Mapped " + geneName + " to " + s);
return s;
} else if (this.taxonMap != null) {
return taxonMap.get(geneName);
} else {
return geneName;
}
}
/**
* Returns SpeciesIDMapper instance associated with this mapping.
* @return
*/
public SpeciesMapper getSpeciesIdMapper() {
return this.speciesIdMapper;
}
public void checkMapping(List<Tree> trees) {
if (this.taxonMap != null) {
Map<String,String> taxonMap = GlobalMaps.taxonNameMap.taxonMap;
String error = Trees.checkMapping(trees, taxonMap);
if (error != null) {
throw new RuntimeException("Gene trees have a leaf named "
+ error
+ " that hasn't been defined in the mapping file");
}
}
}
/* public BitSet getTaxonBitSet(String speciesName) {
if (speciesName == null || "".equals(speciesName)) {
throw new RuntimeException("Empty name?");
}
return this.speciesBitSet.get(speciesName);
}*/
}