From: Jim Procter <jprocter@issues.jalview.org>
Date: Thu, 23 Jun 2016 13:11:27 +0000 (+0100)
Subject: JAL-2110 clarify javadoc
X-Git-Tag: Release_2_10_0~140^2~5^2~40
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=7c0a81832ad897941f0b06856765df8a04227ad8

JAL-2110 clarify javadoc
---

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index 7dcaa17..2c5393d 100644
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -125,6 +125,9 @@ public class CrossRef
    * 
    * @param seq
    *          the sequence whose dbrefs we are searching against
+   * @param fromDna
+   *          when true, context is DNA - so sources identifying protein
+   *          products will be returned.
    * @param sources
    *          a list of sources to add matches to
    */
@@ -762,7 +765,16 @@ public class CrossRef
    * @param cf
    *          a set of sequence mappings to add to
    * @param direct
-   *          - search all references or only subset
+   *          - indicates the type of relationship between returned sequences,
+   *          xrf, and sequenceI that is required.
+   *          <ul>
+   *          <li>direct implies xrf is a primary reference for sequenceI AND
+   *          the sequences to be located (eg a uniprot ID for a protein
+   *          sequence, and a uniprot ref on a transcript sequence).</li>
+   *          <li>indirect means xrf is a cross reference with respect to
+   *          sequenceI or all the returned sequences (eg a genomic reference
+   *          associated with a locus and one or more transcripts)</li>
+   *          </ul>
    * @return true if relationship found and sequence added.
    */
   boolean searchDataset(boolean fromDna, SequenceI sequenceI,