import java.util.TreeSet;
import org.forester.util.ForesterUtil;
-import org.forester.util.SequenceIdParser;
+import org.forester.util.SequenceAccessionTools;
class PrintableSpeciesSpecificDcData implements SpeciesSpecificDcData {
public StringBuffer toStringBuffer( final DomainSimilarityCalculator.Detailedness detailedness, final boolean html ) {
final StringBuffer sb = new StringBuffer();
if ( detailedness == DomainSimilarityCalculator.Detailedness.PUNCTILIOUS ) {
- sb.append( " " );
+ if ( html ) {
+ //sb.append( " " );
+ sb.append( "<td>" );
+ }
sb.append( getKeyDomainDomainsCount() );
- sb.append( ", " );
- sb.append( getKeyDomainProteinsCount() );
- sb.append( ", " );
- sb.append( getCombinableDomainsCount() );
- if ( !getCombinableDomainIdToCountsMap().isEmpty() ) {
- sb.append( ":" );
+ if ( html ) {
+ //sb.append( ", " );
+ sb.append( "</td><td>" );
}
- }
- final Set<String> ids = getCombinableDomainIdToCountsMap().keySet();
- int i = 0;
- for( final String domain_id : ids ) {
- ++i;
- sb.append( " " );
+ else {
+ sb.append( "\t" );
+ }
+ sb.append( getKeyDomainProteinsCount() );
if ( html ) {
- sb.append( "<a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + domain_id + "\">" + domain_id
- + "</a>" );
+ // sb.append( ", " );
+ sb.append( "</td><td>" );
}
else {
- sb.append( domain_id );
+ sb.append( "\t" );
}
- if ( detailedness == DomainSimilarityCalculator.Detailedness.PUNCTILIOUS ) {
- sb.append( ":" );
- sb.append( getCombinableDomainIdToCountsMap().get( domain_id ) );
+ sb.append( getCombinableDomainsCount() );
+ if ( html /*&& !getCombinableDomainIdToCountsMap().isEmpty()*/) {
+ // sb.append( ":" );
+ sb.append( "</td><td>" );
}
}
- sb.append( " [" );
- boolean first = true;
- for( final String p : getKeyDomainProteins() ) {
- final String link = obtainSeqLink( p );
- if ( first ) {
- first = false;
+ if ( html ) {
+ final Set<String> ids = getCombinableDomainIdToCountsMap().keySet();
+ for( final String domain_id : ids ) {
+ sb.append( " " );
+ if ( html ) {
+ sb.append( "<a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + domain_id + "\">" + domain_id
+ + "</a>" );
+ }
+ else {
+ sb.append( domain_id );
+ }
+ if ( detailedness == DomainSimilarityCalculator.Detailedness.PUNCTILIOUS ) {
+ sb.append( ":" );
+ sb.append( getCombinableDomainIdToCountsMap().get( domain_id ) );
+ }
}
- else {
- sb.append( ", " );
+ sb.append( " [" );
+ boolean first = true;
+ for( final String p : getKeyDomainProteins() ) {
+ final String link = obtainSeqLink( p );
+ if ( first ) {
+ first = false;
+ }
+ else {
+ sb.append( ", " );
+ }
+ sb.append( link );
}
- sb.append( link );
+ sb.append( "]" );
+ sb.append( "</td>" );
}
- sb.append( "]" );
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>";