JAL-2738 tidy Javadoc, remove debug logging

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 9680766..1905f42 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -713,7 +713,7 @@ public class Sequence extends ASequence implements SequenceI
             @Override
             public String getChromosomeId()
             {
-              // strip of "chromosome:" prefix to chrId
+              // strip off "chromosome:" prefix to chrId
               return ref.getAccessionId().substring(
                       DBRefEntry.CHROMOSOME.length() + 1);
             }

diff --git a/src/jalview/ext/ensembl/EnsemblSymbol.java b/src/jalview/ext/ensembl/EnsemblSymbol.java
index 75598a0..65be906 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblSymbol.java
+++ b/src/jalview/ext/ensembl/EnsemblSymbol.java
@@ -152,7 +152,6 @@ public class EnsemblSymbol extends EnsemblXref
             if (br != null)
             {
               String geneId = parseSymbolResponse(br);
-              System.out.println(url + " returned " + geneId);
               if (geneId != null && !result.contains(geneId))
               {
                 result.add(geneId);

diff --git a/src/jalview/gui/CrossRefAction.java b/src/jalview/gui/CrossRefAction.java
index 21a0a84..285e574 100644 (file)
--- a/src/jalview/gui/CrossRefAction.java
+++ b/src/jalview/gui/CrossRefAction.java
@@ -336,7 +336,7 @@ public class CrossRefAction implements Runnable
 
     /*
      * hack: ignore cross-references to Ensembl protein ids
-     * (can't fetch chromosomal mapping for these)
+     * (or use map/translation perhaps?)
      * todo: is there an equivalent in EnsemblGenomes?
      */
     if (accession.startsWith("ENSP"))