X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsurfacing%2FPrintableSpeciesSpecificDcData.java;h=56d023989a4810dfd64799abd51c6b297de8ee1d;hb=e836cdba7ba52df7a886c72842beaaf9a3eea699;hp=e54142f5f3e47388496496e498520879151162da;hpb=744ab7983b8a0f44836b97c63d18ed618ed6b28e;p=jalview.git
diff --git a/forester/java/src/org/forester/surfacing/PrintableSpeciesSpecificDcData.java b/forester/java/src/org/forester/surfacing/PrintableSpeciesSpecificDcData.java
index e54142f..56d0239 100644
--- a/forester/java/src/org/forester/surfacing/PrintableSpeciesSpecificDcData.java
+++ b/forester/java/src/org/forester/surfacing/PrintableSpeciesSpecificDcData.java
@@ -34,7 +34,7 @@ import java.util.TreeMap;
import java.util.TreeSet;
import org.forester.util.ForesterUtil;
-import org.forester.util.SequenceIdParser;
+import org.forester.util.SequenceAccessionTools;
class PrintableSpeciesSpecificDcData implements SpeciesSpecificDcData {
@@ -97,46 +97,63 @@ 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( "
" );
+ }
sb.append( getKeyDomainDomainsCount() );
- sb.append( ", " );
- sb.append( getKeyDomainProteinsCount() );
- sb.append( ", " );
- sb.append( getCombinableDomainsCount() );
- if ( !getCombinableDomainIdToCountsMap().isEmpty() ) {
- sb.append( ":" );
+ if ( html ) {
+ //sb.append( ", " );
+ sb.append( " | " );
}
- }
- final Set 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( "" + domain_id
- + "" );
+ // sb.append( ", " );
+ sb.append( " | " );
}
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( " | " );
}
}
- sb.append( " [" );
- boolean first = true;
- for( final String p : getKeyDomainProteins() ) {
- final String link = obtainSeqLink( p );
- if ( first ) {
- first = false;
+ if ( html ) {
+ final Set ids = getCombinableDomainIdToCountsMap().keySet();
+ for( final String domain_id : ids ) {
+ sb.append( " " );
+ if ( html ) {
+ sb.append( "" + domain_id
+ + "" );
+ }
+ 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( " | " );
}
- sb.append( "]" );
return sb;
}
@@ -154,19 +171,19 @@ class PrintableSpeciesSpecificDcData implements SpeciesSpecificDcData {
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 = "" + up_id
+ "";
}
else {
- final String gb_id = SequenceIdParser.parseGenbankProteinAccessor( p );
+ final String gb_id = SequenceAccessionTools.parseGenbankProteinAccessorFromString( p );
if ( !ForesterUtil.isEmpty( gb_id ) ) {
link = ""
+ gb_id + "";
}
else {
- final String gi = SequenceIdParser.parseGInumber( p );
+ final String gi = SequenceAccessionTools.parseGInumberFromString( p );
if ( !ForesterUtil.isEmpty( gi ) ) {
link = "gi|" + gi
+ "";