inprogress

[jalview.git] / forester / java / src / org / forester / surfacing / PrintableSpeciesSpecificDcData.java

diff --git a/forester/java/src/org/forester/surfacing/PrintableSpeciesSpecificDcData.java b/forester/java/src/org/forester/surfacing/PrintableSpeciesSpecificDcData.java
index 79dcb37..be2fcc7 100644 (file)
--- a/forester/java/src/org/forester/surfacing/PrintableSpeciesSpecificDcData.java
+++ b/forester/java/src/org/forester/surfacing/PrintableSpeciesSpecificDcData.java
@@ -34,13 +34,14 @@ import java.util.TreeMap;
 import java.util.TreeSet;
 
 import org.forester.util.ForesterUtil;
+import org.forester.util.SequenceAccessionTools;
 
 class PrintableSpeciesSpecificDcData implements SpeciesSpecificDcData {
 
     final SortedMap<String, Integer> _combinable_domain_id_to_count_map;
     final SortedSet<String>          _key_domain_proteins;
-    final private int                _key_domain_domains_count;
     final private int                _combinable_domains_count;
+    final private int                _key_domain_domains_count;
 
     public PrintableSpeciesSpecificDcData( final int key_domain_domains_count, final int combinable_domains ) {
         _key_domain_proteins = new TreeSet<String>();
@@ -50,6 +51,17 @@ class PrintableSpeciesSpecificDcData implements SpeciesSpecificDcData {
     }
 
     @Override
+    public void addKeyDomainProtein( final String protein ) {
+        if ( ForesterUtil.isEmpty( protein ) ) {
+            throw new IllegalArgumentException( "attempt to add null or empty protein" );
+        }
+        if ( getKeyDomainProteins().contains( protein ) ) {
+            throw new IllegalArgumentException( "protein \"" + protein + "\" is not unique" );
+        }
+        getKeyDomainProteins().add( protein );
+    }
+
+    @Override
     public void addProteinsExhibitingCombinationCount( final String domain_id, final int count ) {
         if ( getCombinableDomainIdToCountsMap().containsKey( domain_id ) ) {
             throw new IllegalArgumentException( "Domain with id " + domain_id + " already exists" );
@@ -62,16 +74,9 @@ class PrintableSpeciesSpecificDcData implements SpeciesSpecificDcData {
         return _combinable_domain_id_to_count_map;
     }
 
-    private int getCombinableDomainsCount() {
-        return _combinable_domains_count;
-    }
-
-    private int getKeyDomainDomainsCount() {
-        return _key_domain_domains_count;
-    }
-
-    private int getKeyDomainProteinsCount() {
-        return _key_domain_proteins.size();
+    @Override
+    public SortedSet<String> getKeyDomainProteins() {
+        return _key_domain_proteins;
     }
 
     @Override
@@ -83,22 +88,6 @@ class PrintableSpeciesSpecificDcData implements SpeciesSpecificDcData {
     }
 
     @Override
-    public void addKeyDomainProtein( final String protein ) {
-        if ( ForesterUtil.isEmpty( protein ) ) {
-            throw new IllegalArgumentException( "attempt to add null or empty protein" );
-        }
-        if ( getKeyDomainProteins().contains( protein ) ) {
-            throw new IllegalArgumentException( "protein \"" + protein + "\" is not unique" );
-        }
-        getKeyDomainProteins().add( protein );
-    }
-
-    @Override
-    public SortedSet<String> getKeyDomainProteins() {
-        return _key_domain_proteins;
-    }
-
-    @Override
     public String toString() {
         return toStringBuffer( DomainSimilarityCalculator.Detailedness.LIST_COMBINING_DOMAIN_FOR_EACH_SPECIES, false )
                 .toString();
@@ -108,53 +97,103 @@ 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() ) {
-            String link = null;
-            final String up_id = ForesterUtil.extractUniProtKbProteinSeqIdentifier( p );
-            if ( !ForesterUtil.isEmpty( up_id ) ) {
-                link = "<a href=\"" + ForesterUtil.UNIPROT_KB + up_id + "\" target=\"_up_window\">" + up_id + "</a>";
+        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 {
-                link = "<a href=\"" + "http://www.google.com/search?q=" + p + "\" target=\"_g_window\">" + p + "</a>";
+            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 );
             }
-            if ( first ) {
-                first = false;
+            sb.append( "]" );
+            sb.append( "</td>" );
+        }
+        return sb;
+    }
+
+    private int getCombinableDomainsCount() {
+        return _combinable_domains_count;
+    }
+
+    private int getKeyDomainDomainsCount() {
+        return _key_domain_domains_count;
+    }
+
+    private int getKeyDomainProteinsCount() {
+        return _key_domain_proteins.size();
+    }
+
+    private static String obtainSeqLink( final String p ) {
+        String link;
+        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 = 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 {
-                sb.append( ", " );
+                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>";
+                }
+                else {
+                    link = "<a class=\"ps\" href=\"" + "http://www.google.com/search?q=" + p
+                            + "\" target=\"_g_window\">" + p + "</a>";
+                }
             }
-            sb.append( p );
         }
-        sb.append( "]" );
-        return sb;
+        return link;
     }
 }