From 908bf85e4afe1e303515797719df5dd8afec06e7 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Mon, 28 Mar 2016 10:12:36 +0100 Subject: [PATCH] JAL-1705 Javadoc / debug output tweaks --- src/jalview/datamodel/AlignedCodonFrame.java | 9 +++++++++ src/jalview/datamodel/SequenceFeature.java | 6 ++++++ src/jalview/datamodel/xdb/embl/EmblEntry.java | 6 +++--- src/jalview/ws/SequenceFetcher.java | 4 +--- 4 files changed, 19 insertions(+), 6 deletions(-) diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java index 3fc8c28..179f5cc 100644 --- a/src/jalview/datamodel/AlignedCodonFrame.java +++ b/src/jalview/datamodel/AlignedCodonFrame.java @@ -638,4 +638,13 @@ public class AlignedCodonFrame { return mappings.isEmpty(); } + + /** + * Method for debug / inspection purposes only, may change in future + */ + @Override + public String toString() + { + return mappings == null ? "null" : mappings.toString(); + } } diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java index 8146400..4a7706f 100755 --- a/src/jalview/datamodel/SequenceFeature.java +++ b/src/jalview/datamodel/SequenceFeature.java @@ -423,6 +423,12 @@ public class SequenceFeature return strand; } + /** + * Set the value of strand + * + * @param strand + * should be "+" for forward, or "-" for reverse + */ public void setStrand(String strand) { setValue(STRAND, strand); diff --git a/src/jalview/datamodel/xdb/embl/EmblEntry.java b/src/jalview/datamodel/xdb/embl/EmblEntry.java index d830130..fda042e 100644 --- a/src/jalview/datamodel/xdb/embl/EmblEntry.java +++ b/src/jalview/datamodel/xdb/embl/EmblEntry.java @@ -708,9 +708,9 @@ public class EmblEntry sxpos = x; if (cdslength != cdspos) { - System.err - .println("Truncating final exon interval on region by " - + (cdspos - cdslength)); + // System.err + // .println("Truncating final exon interval on region by " + // + (cdspos - cdslength)); } // locate the new end boundary of final exon as endxon endxon = exon[x + 1] - cdspos + cdslength; diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java index 902ce27..1f8c28a 100644 --- a/src/jalview/ws/SequenceFetcher.java +++ b/src/jalview/ws/SequenceFetcher.java @@ -39,9 +39,7 @@ import java.util.ArrayList; import java.util.List; /** - * This is the the concrete implementation of the sequence retrieval interface - * and abstract class in jalview.ws.seqfetcher. This implements the run-time - * discovery of sequence database clientss. + * This implements the run-time discovery of sequence database clients. * */ public class SequenceFetcher extends ASequenceFetcher -- 1.7.10.2