From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 28 Mar 2016 09:12:36 +0000 (+0100)
Subject: JAL-1705 Javadoc / debug output tweaks
X-Git-Tag: Release_2_10_0~270^2~1^2~11
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=908bf85e4afe1e303515797719df5dd8afec06e7;p=jalview.git

JAL-1705 Javadoc / debug output tweaks
---

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