import java.util.TreeSet;
import org.forester.util.ForesterUtil;
-import org.forester.util.SequenceIdParser;
+import org.forester.util.SequenceAccessionTools;
class PrintableSpeciesSpecificDcData implements SpeciesSpecificDcData {
final StringBuffer sb = new StringBuffer();
if ( detailedness == DomainSimilarityCalculator.Detailedness.PUNCTILIOUS ) {
if ( html ) {
- sb.append( " " );
+ //sb.append( " " );
+ sb.append( "<td>" );
}
sb.append( getKeyDomainDomainsCount() );
if ( html ) {
- sb.append( ", " );
+ //sb.append( ", " );
+ sb.append( "</td><td>" );
}
else {
sb.append( "\t" );
}
sb.append( getKeyDomainProteinsCount() );
if ( html ) {
- sb.append( ", " );
+ // sb.append( ", " );
+ sb.append( "</td><td>" );
}
else {
sb.append( "\t" );
}
sb.append( getCombinableDomainsCount() );
- if ( html && !getCombinableDomainIdToCountsMap().isEmpty() ) {
- sb.append( ":" );
+ if ( html /*&& !getCombinableDomainIdToCountsMap().isEmpty()*/) {
+ // sb.append( ":" );
+ sb.append( "</td><td>" );
}
}
if ( html ) {
final Set<String> ids = getCombinableDomainIdToCountsMap().keySet();
- int i = 0;
for( final String domain_id : ids ) {
- ++i;
sb.append( " " );
if ( html ) {
sb.append( "<a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + domain_id + "\">" + domain_id
sb.append( link );
}
sb.append( "]" );
+ sb.append( "</td>" );
}
return sb;
}
private static String obtainSeqLink( final String p ) {
String link;
- final String up_id = ForesterUtil.extractUniProtKbProteinSeqIdentifier( p );
+ final String up_id = SequenceAccessionTools.parseUniProtAccessorFromString( p );
if ( !ForesterUtil.isEmpty( up_id ) ) {
link = "<a class=\"pl\" href=\"" + ForesterUtil.UNIPROT_KB + up_id + "\" target=\"_up_window\">" + up_id
+ "</a>";
}
else {
- final String gb_id = SequenceIdParser.parseGenbankProteinAccessor( p );
+ final String gb_id = SequenceAccessionTools.parseGenbankProteinAccessorFromString( p );
if ( !ForesterUtil.isEmpty( gb_id ) ) {
link = "<a class=\"pl\" href=\"" + ForesterUtil.NCBI_PROTEIN + gb_id + "\" target=\"_up_window\">"
+ gb_id + "</a>";
}
else {
- final String gi = SequenceIdParser.parseGInumber( p );
+ final String gi = SequenceAccessionTools.parseGInumberFromString( p );
if ( !ForesterUtil.isEmpty( gi ) ) {
link = "<a class=\"pl\" href=\"" + ForesterUtil.NCBI_GI + gi + "\" target=\"_up_window\">gi|" + gi
+ "</a>";