From a75627585f245e8fe0575ce92492c1ccde9b41d5 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Tue, 24 Oct 2017 17:02:58 +0100 Subject: [PATCH] JAL-2738 tidy Javadoc, remove debug logging --- src/jalview/datamodel/Sequence.java | 2 +- src/jalview/ext/ensembl/EnsemblSymbol.java | 1 - src/jalview/gui/CrossRefAction.java | 2 +- 3 files changed, 2 insertions(+), 3 deletions(-) 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")) -- 1.7.10.2