final int s = species_data.size();
if ( ( ( s * s ) - s ) != ( getN() * 2 ) ) {
throw new IllegalArgumentException( "illegal species count and n: species count:" + s + ", n:" + _n
- + " for domain " + combinable_domains.getKeyDomain() );
+ + " for domain " + combinable_domains.getKeyDomain() );
}
if ( s > 2 ) {
if ( getMaximalDifferenceInCounts() < 0 ) {
}
}
+ @Override
public int compareTo( final DomainSimilarity domain_similarity ) {
if ( this == domain_similarity ) {
return EQUAL;
/**
* For pairwise similarities, this should return the "difference"; for example the difference in counts
* for copy number based features (the same as getMaximalDifferenceInCounts(), or the number
- * of actually different domain combinations.
+ * of actually different domain combinations.
* For pairwise similarities, this should return the difference,
* while for comparisons of more than two domains, this should return the maximal difference
- *
+ *
*/
public int getMaximalDifference() {
return _max_difference;
* For pairwise similarities, this should return the difference in counts,
* while for comparisons of more than two domains, this should return the maximal difference
* in counts
- *
- *
+ *
+ *
* @return the (maximal) difference in counts
*/
public int getMaximalDifferenceInCounts() {
/**
* This should return the number of pairwise distances used to calculate
* this similarity score
- *
+ *
* @return the number of pairwise distances
*/
public int getN() {
/**
* This should return a map, which maps species names to
* SpeciesSpecificDomainSimilariyData
- *
- *
+ *
+ *
* @return SortedMap<String, SpeciesSpecificDomainSimilariyData>
*/
public SortedMap<Species, SpeciesSpecificDcData> getSpeciesData() {
sb.append( "</td>" );
sb.append( "<td>" );
sb.append( "<a href=\"" + SurfacingConstants.GOOGLE_SCHOLAR_SEARCH + getDomainId()
- + "\" target=\"gs_window\">gs</a>" );
+ + "\" target=\"gs_window\">gs</a>" );
sb.append( "</td>" );
if ( getMaximalSimilarityScore() > 0 ) {
sb.append( "<td>" );
_base = base;
}
+ @Override
public int compare( final String a, final String b ) {
if ( _base.get( a ) >= _base.get( b ) ) {
return -1;