import java.util.TreeMap;
import org.forester.protein.Domain;
-import org.forester.protein.DomainId;
import org.forester.protein.Protein;
import org.forester.species.Species;
import org.forester.util.BasicDescriptiveStatistics;
public class DomainLengthsTable {
- private final static DecimalFormat DF = new DecimalFormat( "#.0" );
- final SortedMap<DomainId, DomainLengths> _domain_lengths;
- final List<Species> _species;
+ private final static DecimalFormat DF = new DecimalFormat( "#.0" );
+ final SortedMap<String, DomainLengths> _domain_lengths;
+ final List<Species> _species;
public DomainLengthsTable() {
- _domain_lengths = new TreeMap<DomainId, DomainLengths>();
+ _domain_lengths = new TreeMap<String, DomainLengths>();
_species = new ArrayList<Species>();
}
- private void addDomainLengths( final DomainLengths domain_lengths ) {
- if ( getDomainLengths().containsKey( domain_lengths.getDomainId() ) ) {
- throw new IllegalArgumentException( "domain lengths for [" + domain_lengths.getDomainId()
- + "] already added" );
- }
- getDomainLengths().put( domain_lengths.getDomainId(), domain_lengths );
- }
-
- private void addLength( final DomainId domain_id, final Species species, final int domain_length ) {
- if ( !getDomainLengths().containsKey( domain_id ) ) {
- addDomainLengths( new DomainLengths( domain_id ) );
- }
- getDomainLengths().get( domain_id ).addLength( species, domain_length );
- }
-
public void addLengths( final List<Protein> protein_list ) {
for( final Protein protein : protein_list ) {
final Species species = protein.getSpecies();
return stats;
}
- public DescriptiveStatistics calculateMeanBasedStatisticsForDomain( final DomainId domain_id ) {
+ public DescriptiveStatistics calculateMeanBasedStatisticsForDomain( final String domain_id ) {
return getDomainLengths( domain_id ).calculateMeanBasedStatistics();
}
return sb;
}
- private SortedMap<DomainId, DomainLengths> getDomainLengths() {
- return _domain_lengths;
- }
-
- public DomainLengths getDomainLengths( final DomainId domain_id ) {
+ public DomainLengths getDomainLengths( final String domain_id ) {
return getDomainLengths().get( domain_id );
}
return list;
}
- public DescriptiveStatistics getLengthStatistic( final DomainId domain_id, final Species species ) {
+ public DescriptiveStatistics getLengthStatistic( final String domain_id, final Species species ) {
return getDomainLengths( domain_id ).getLengthStatistic( species );
}
public List<Species> getSpecies() {
return _species;
}
+
+ private void addDomainLengths( final DomainLengths domain_lengths ) {
+ if ( getDomainLengths().containsKey( domain_lengths.getDomainId() ) ) {
+ throw new IllegalArgumentException( "domain lengths for [" + domain_lengths.getDomainId()
+ + "] already added" );
+ }
+ getDomainLengths().put( domain_lengths.getDomainId(), domain_lengths );
+ }
+
+ private void addLength( final String domain_id, final Species species, final int domain_length ) {
+ if ( !getDomainLengths().containsKey( domain_id ) ) {
+ addDomainLengths( new DomainLengths( domain_id ) );
+ }
+ getDomainLengths().get( domain_id ).addLength( species, domain_length );
+ }
+
+ private SortedMap<String, DomainLengths> getDomainLengths() {
+ return _domain_lengths;
+ }
}