From eb3461a71b073a0e7a9a2dba6481b5ed3fca71e9 Mon Sep 17 00:00:00 2001
From: Jim Procter <j.procter@dundee.ac.uk>
Date: Thu, 22 Jul 2021 18:04:01 +0100
Subject: [PATCH] =?utf8?q?JAL-3848=20ensure=20annotation=20from=20a=20servic?=
 =?utf8?q?e=20gets=20a=20calcId=20so=20it=20can=20be=20updated=20and=20track?=
 =?utf8?q?ed=20across=20multiple=20views=20-=20nb=20-=20service.getId()=20pr?=
 =?utf8?q?obably=20isn=E2=80=99t=20the=20right=20value=20to=20use=20for=20th?=
 =?utf8?q?is!?=
MIME-Version: 1.0
Content-Type: text/plain; charset=utf8
Content-Transfer-Encoding: 8bit

---
 src/jalview/io/AnnotationFile.java                 |   23 +++++++++++++++++++-
 .../slivkaws/SlivkaAnnotationServiceInstance.java  |    2 +-
 2 files changed, 23 insertions(+), 2 deletions(-)

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 2182b24..9daae63 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -33,6 +33,7 @@ import java.util.Vector;
 
 import jalview.analysis.Conservation;
 import jalview.api.AlignViewportI;
+import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
@@ -65,6 +66,11 @@ public class AnnotationFile
   private String lastread = "";
 
   /**
+   * default calcId string for new annotation
+   */
+  private String defaultCalcId = null;
+
+  /**
    * Constructor
    */
   public AnnotationFile()
@@ -664,6 +670,21 @@ public class AnnotationFile
     return readAnnotationFile(al, null, file, sourceType);
   }
 
+  /**
+   * read an annotation file onto the alignment, but apply the given calcId
+   * @param aln
+   * @param calcId
+   * @param file
+   * @param url
+   * @return
+   */
+  public boolean readAnnotationFileWithCalcId(Alignment aln, String calcId, String file,
+          DataSourceType url)
+  {
+    defaultCalcId=calcId;
+    return readAnnotationFile(aln, null, file, url);
+  }
+  
   public boolean readAnnotationFile(AlignmentI al, HiddenColumns hidden,
           Object file, DataSourceType sourceType)
   {
@@ -1004,7 +1025,7 @@ public class AnnotationFile
 
         annotation = new AlignmentAnnotation(label, description,
                 (index == 0) ? null : annotations, 0, 0, graphStyle);
-
+        annotation.setCalcId(defaultCalcId);
         annotation.score = score;
         if (!overrideAutoAnnot && autoAnnots
                 .containsKey(autoAnnotsKey(annotation, refSeq, groupRef)))
diff --git a/src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java b/src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java
index 3c80fbc..c42d42e 100644
--- a/src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java
+++ b/src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java
@@ -83,7 +83,7 @@ public class SlivkaAnnotationServiceInstance extends SlivkaWSInstance implements
     }
     Alignment aln = new Alignment(seqs.toArray(new SequenceI[0]));
     if (annotFile == null
-        || !new AnnotationFile().readAnnotationFile(aln, annotFile.getContentUrl().toString(), DataSourceType.URL))
+        || !new AnnotationFile().readAnnotationFileWithCalcId(aln, service.getId(), annotFile.getContentUrl().toString(), DataSourceType.URL))
     {
       Cache.log.debug("No annotation from slivka job\n" + annotFile);
     }
-- 
1.7.10.2