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 ) {
/**
* 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() {
final Map<String, Integer> tax_code_to_id_map,
final Phylogeny phy ) {
final StringBuffer sb = new StringBuffer();
- sb.append( "<table>" );
+ if (html) {
+ sb.append( "<table>" );
+ }
for( final Species species : getSpeciesData().keySet() ) {
addSpeciesSpecificDomainData( sb, species, html, tax_code_to_id_map, phy );
}
- sb.append( "</table>" );
+ if (html) {
+ sb.append( "</table>" );
+ }
return sb;
}
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>" );