X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsurfacing%2FDomainSimilarity.java;h=1c65f1c7621d11ed2c7735827d77cff17c889017;hb=d605114bdf420c6cb680b02bb10ea25f09db769c;hp=144e3b84daf0ea392beb8b47289f91658d122826;hpb=7e567e18a5ba32035a8db4ca041023c9e862d25b;p=jalview.git

diff --git a/forester/java/src/org/forester/surfacing/DomainSimilarity.java b/forester/java/src/org/forester/surfacing/DomainSimilarity.java
index 144e3b8..1c65f1c 100644
--- a/forester/java/src/org/forester/surfacing/DomainSimilarity.java
+++ b/forester/java/src/org/forester/surfacing/DomainSimilarity.java
@@ -110,7 +110,7 @@ public class DomainSimilarity implements Comparable<DomainSimilarity> {
         final int s = species_data.size();
         if ( ( ( s * s ) - s ) != ( getN() * 2 ) ) {
             throw new IllegalArgumentException( "illegal species count and n: species count:" + s + ", n:" + _n
-                    + " for domain " + combinable_domains.getKeyDomain() );
+                                                + " for domain " + combinable_domains.getKeyDomain() );
         }
         if ( s > 2 ) {
             if ( getMaximalDifferenceInCounts() < 0 ) {
@@ -192,10 +192,10 @@ public class DomainSimilarity implements Comparable<DomainSimilarity> {
     /**
      * For pairwise similarities, this should return the "difference"; for example the difference in counts
      * for copy number based features (the same as getMaximalDifferenceInCounts(), or the number
-     * of actually different domain combinations. 
+     * of actually different domain combinations.
      * For pairwise similarities, this should return the difference,
      * while for comparisons of more than two domains, this should return the maximal difference
-     * 
+     *
      */
     public int getMaximalDifference() {
         return _max_difference;
@@ -205,8 +205,8 @@ public class DomainSimilarity implements Comparable<DomainSimilarity> {
      * For pairwise similarities, this should return the difference in counts,
      * while for comparisons of more than two domains, this should return the maximal difference
      * in counts
-     * 
-     * 
+     *
+     *
      * @return the (maximal) difference in counts
      */
     public int getMaximalDifferenceInCounts() {
@@ -228,7 +228,7 @@ public class DomainSimilarity implements Comparable<DomainSimilarity> {
     /**
      * This should return the number of pairwise distances used to calculate
      * this similarity score
-     * 
+     *
      * @return the number of pairwise distances
      */
     public int getN() {
@@ -250,8 +250,8 @@ public class DomainSimilarity implements Comparable<DomainSimilarity> {
     /**
      * This should return a map, which maps species names to
      * SpeciesSpecificDomainSimilariyData
-     * 
-     * 
+     *
+     *
      * @return SortedMap<String, SpeciesSpecificDomainSimilariyData>
      */
     public SortedMap<Species, SpeciesSpecificDcData> getSpeciesData() {
@@ -405,11 +405,15 @@ public class DomainSimilarity implements Comparable<DomainSimilarity> {
                                                             final Map<String, Integer> tax_code_to_id_map,
                                                             final Phylogeny phy ) {
         final StringBuffer sb = new StringBuffer();
-        sb.append( "<table>" );
+        if (html) {
+            sb.append( "<table>" );
+        }
         for( final Species species : getSpeciesData().keySet() ) {
             addSpeciesSpecificDomainData( sb, species, html, tax_code_to_id_map, phy );
         }
-        sb.append( "</table>" );
+        if (html) {
+            sb.append( "</table>" );
+        }
         return sb;
     }
 
@@ -538,7 +542,7 @@ public class DomainSimilarity implements Comparable<DomainSimilarity> {
         sb.append( "</td>" );
         sb.append( "<td>" );
         sb.append( "<a href=\"" + SurfacingConstants.GOOGLE_SCHOLAR_SEARCH + getDomainId()
-                + "\" target=\"gs_window\">gs</a>" );
+                   + "\" target=\"gs_window\">gs</a>" );
         sb.append( "</td>" );
         if ( getMaximalSimilarityScore() > 0 ) {
             sb.append( "<td>" );