From: gmungoc Date: Tue, 24 Oct 2017 16:02:58 +0000 (+0100) Subject: JAL-2738 tidy Javadoc, remove debug logging X-Git-Tag: Release_2_11_0~185 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a75627585f245e8fe0575ce92492c1ccde9b41d5;p=jalview.git 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 --- 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 --- 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 --- 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"))