X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsurfacing%2FPrintableSpeciesSpecificDcData.java;h=56d023989a4810dfd64799abd51c6b297de8ee1d;hb=8d6e81da091d432309f2f7034cf93dbc5ba5e82a;hp=26cb4334675b2b0539f191096d122ac9619be9b8;hpb=3171b9b28762e02b3fbd9b5f8a5b1946497f2178;p=jalview.git
diff --git a/forester/java/src/org/forester/surfacing/PrintableSpeciesSpecificDcData.java b/forester/java/src/org/forester/surfacing/PrintableSpeciesSpecificDcData.java
index 26cb433..56d0239 100644
--- a/forester/java/src/org/forester/surfacing/PrintableSpeciesSpecificDcData.java
+++ b/forester/java/src/org/forester/surfacing/PrintableSpeciesSpecificDcData.java
@@ -98,36 +98,38 @@ class PrintableSpeciesSpecificDcData implements SpeciesSpecificDcData {
final StringBuffer sb = new StringBuffer();
if ( detailedness == DomainSimilarityCalculator.Detailedness.PUNCTILIOUS ) {
if ( html ) {
- sb.append( " " );
+ //sb.append( " " );
+ sb.append( "
" );
}
sb.append( getKeyDomainDomainsCount() );
if ( html ) {
- sb.append( ", " );
+ //sb.append( ", " );
+ sb.append( " | " );
}
else {
sb.append( "\t" );
}
sb.append( getKeyDomainProteinsCount() );
if ( html ) {
- sb.append( ", " );
+ // sb.append( ", " );
+ sb.append( " | " );
}
else {
sb.append( "\t" );
}
sb.append( getCombinableDomainsCount() );
- if ( html && !getCombinableDomainIdToCountsMap().isEmpty() ) {
- sb.append( ":" );
+ if ( html /*&& !getCombinableDomainIdToCountsMap().isEmpty()*/) {
+ // sb.append( ":" );
+ sb.append( " | " );
}
}
if ( html ) {
final Set ids = getCombinableDomainIdToCountsMap().keySet();
- int i = 0;
for( final String domain_id : ids ) {
- ++i;
sb.append( " " );
if ( html ) {
sb.append( "" + domain_id
- + "" );
+ + "" );
}
else {
sb.append( domain_id );
@@ -150,6 +152,7 @@ class PrintableSpeciesSpecificDcData implements SpeciesSpecificDcData {
sb.append( link );
}
sb.append( "]" );
+ sb.append( " | " );
}
return sb;
}
@@ -168,19 +171,19 @@ class PrintableSpeciesSpecificDcData implements SpeciesSpecificDcData {
private static String obtainSeqLink( final String p ) {
String link;
- final String up_id = SequenceAccessionTools.extractUniProtKbProteinSeqIdentifier( p );
+ final String up_id = SequenceAccessionTools.parseUniProtAccessorFromString( p );
if ( !ForesterUtil.isEmpty( up_id ) ) {
link = "" + up_id
+ "";
}
else {
- final String gb_id = SequenceAccessionTools.parseGenbankProteinAccessor( p );
+ final String gb_id = SequenceAccessionTools.parseGenbankProteinAccessorFromString( p );
if ( !ForesterUtil.isEmpty( gb_id ) ) {
link = ""
+ gb_id + "";
}
else {
- final String gi = SequenceAccessionTools.parseGInumber( p );
+ final String gi = SequenceAccessionTools.parseGInumberFromString( p );
if ( !ForesterUtil.isEmpty( gi ) ) {
link = "gi|" + gi
+ "";