From: Mateusz Warowny <mmzwarowny@dundee.ac.uk>
Date: Fri, 28 Jul 2023 10:37:32 +0000 (+0200)
Subject:  --- Adding issue comments
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ab58313e7bb31264ddb2715a1c548cdc789d7fa6;p=jalview.git

 --- Adding issue comments
---

diff --git a/src/jalview/ws/jws2/SeqAnnotationServiceCalcWorker.java b/src/jalview/ws/jws2/SeqAnnotationServiceCalcWorker.java
index 3253f43..fee2b38 100644
--- a/src/jalview/ws/jws2/SeqAnnotationServiceCalcWorker.java
+++ b/src/jalview/ws/jws2/SeqAnnotationServiceCalcWorker.java
@@ -712,11 +712,18 @@ public class SeqAnnotationServiceCalcWorker extends AlignCalcWorker
           SequenceI seq = running.getSeqNames()
                   .get(ala.sequenceRef.getName());
           aseq = seq;
+          // This part doesn't do anything. I suppose bad merge.
           while (seq.getDatasetSequence() != null)
           {
             seq = seq.getDatasetSequence();
           }
         }
+        /* Prepare an array for annotations and copy returned annotations to it.
+         * Similar process happens in develop:JabawsCalcWorker#constructAnnotationFromScore.
+         * However, JabawsCalcWorker fills the array form the beginning, not
+         * the start position (start - column of the submitted region).
+         * Also, JabawsCalcWorker adds those annotations to an AlignmentAnnotation
+         * retrieved from the current alignment. */
         Annotation[] resAnnot = ala.annotations,
                 gappedAnnot = new Annotation[Math.max(
                         alignViewport.getAlignment().getWidth(),
@@ -732,6 +739,10 @@ public class SeqAnnotationServiceCalcWorker extends AlignCalcWorker
             gappedAnnot[ap] = resAnnot[p++];
           }
         }
+        /* Annotations are set in-place on the AlignmentAnnotation object returned by the service.
+         * First, if #updateResultAnnotation is called again the output will be mangled
+         * Second, the mapping of positions to annotations held internally by
+         * the `ala` object is now incorrect. */
         ala.sequenceRef = aseq;
         ala.annotations = gappedAnnot;
         AlignmentAnnotation newAnnot = getAlignViewport().getAlignment()
@@ -740,6 +751,12 @@ public class SeqAnnotationServiceCalcWorker extends AlignCalcWorker
         {
 
           aseq.addAlignmentAnnotation(newAnnot);
+          /* adjustForAlignment is meant to move annotations to their columns
+           * according to the sequenceMapping.
+           * Since the mapping is carried from the alignment returned by the
+           * service it simply maps annotations to consecutive positions 1, 2, 3...
+           * Resulting in the annotation row being always aligned to the beginning
+           * of the alignment. */
           newAnnot.adjustForAlignment();
 
           AlignmentAnnotationUtils.replaceAnnotationOnAlignmentWith(