X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentAnnotationUtils.java;h=5c2d9364b92f3947b991fd9bf6f4e190b2a5c1f8;hb=daa1765ab2101480a724b92a3f3e7dee662ba943;hp=9bdbf7352a57513df57587766dc930e0243d5ebc;hpb=eaf9092bfa74b5162589c8775f68a19dd79dbb1d;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentAnnotationUtils.java b/src/jalview/analysis/AlignmentAnnotationUtils.java
index 9bdbf73..5c2d936 100644
--- a/src/jalview/analysis/AlignmentAnnotationUtils.java
+++ b/src/jalview/analysis/AlignmentAnnotationUtils.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.analysis;
 
 import jalview.datamodel.AlignmentAnnotation;
@@ -55,24 +75,31 @@ public class AlignmentAnnotationUtils
      * Build a lookup, by calcId (annotation source), of all annotation types in
      * each graph group.
      */
-    Map<String, Map<Integer, List<String>>> groupLabels = new HashMap<String, Map<Integer, List<String>>>();
+    Map<String, Map<Integer, List<String>>> groupLabels = new HashMap<>();
 
     // trackers for which calcId!label combinations we have dealt with
-    List<String> addedToShown = new ArrayList<String>();
-    List<String> addedToHidden = new ArrayList<String>();
+    List<String> addedToShown = new ArrayList<>();
+    List<String> addedToHidden = new ArrayList<>();
 
     for (AlignmentAnnotation aa : annotations)
     {
-      if (forSequences != null
-              && (aa.sequenceRef != null && forSequences
-                      .contains(aa.sequenceRef)))
+      /*
+       * Ignore non-positional annotations, can't render these against an
+       * alignment
+       */
+      if (aa.annotations == null)
+      {
+        continue;
+      }
+      if (forSequences != null && (aa.sequenceRef != null
+              && forSequences.contains(aa.sequenceRef)))
       {
         String calcId = aa.getCalcId();
 
         /*
          * Build a 'composite label' for types in line graph groups.
          */
-        final List<String> labelAsList = new ArrayList<String>();
+        final List<String> labelAsList = new ArrayList<>();
         final String displayLabel = aa.label;
         labelAsList.add(displayLabel);
         if (aa.graph == AlignmentAnnotation.LINE_GRAPH
@@ -86,8 +113,8 @@ public class AlignmentAnnotationUtils
                   .get(calcId);
           if (groupLabelsForCalcId.containsKey(aa.graphGroup))
           {
-            if (!groupLabelsForCalcId.get(aa.graphGroup).contains(
-                    displayLabel))
+            if (!groupLabelsForCalcId.get(aa.graphGroup)
+                    .contains(displayLabel))
             {
               groupLabelsForCalcId.get(aa.graphGroup).add(displayLabel);
             }
@@ -212,4 +239,42 @@ public class AlignmentAnnotationUtils
     return (anns == null ? Collections.<AlignmentAnnotation> emptyList()
             : Arrays.asList(anns));
   }
+
+  /**
+   * replace an existing sequence associated annotation with another, creating
+   * association as necessary.
+   * 
+   * @param newAnnot
+   *          - annotation row associated with a sequence to be propagated to
+   *          its reference annotation
+   * @param typeName
+   *          - label used to match existing row
+   * @param calcId
+   *          - calcId for existing row
+   */
+  public static void replaceAnnotationOnAlignmentWith(
+          AlignmentAnnotation newAnnot, String typeName, String calcId)
+  {
+    if (newAnnot.sequenceRef != null)
+    {
+      SequenceI dsseq = newAnnot.sequenceRef;
+      while (dsseq.getDatasetSequence() != null)
+      {
+        dsseq = dsseq.getDatasetSequence();
+      }
+      // look for same annotation on dataset and lift this one over
+      List<AlignmentAnnotation> dsan = dsseq.getAlignmentAnnotations(calcId,
+              typeName);
+      if (dsan != null && dsan.size() > 0)
+      {
+        for (AlignmentAnnotation dssan : dsan)
+        {
+          dsseq.removeAlignmentAnnotation(dssan);
+        }
+      }
+      AlignmentAnnotation dssan = new AlignmentAnnotation(newAnnot);
+      dsseq.addAlignmentAnnotation(dssan);
+      dssan.adjustForAlignment();
+    }
+  }
 }