X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentAnnotationUtils.java;h=194ef80354b4d32827db3c08ce40ce7c5b2c9477;hb=c7bc2d0abe568732fd9249c56b98370944a6e43f;hp=ef8e6705d3e4f03ae7528e11fe3348cabd63619b;hpb=ec493e27abc6b3be84b3c8a873c295a3f589bd53;p=jalview.git
diff --git a/src/jalview/analysis/AlignmentAnnotationUtils.java b/src/jalview/analysis/AlignmentAnnotationUtils.java
index ef8e670..194ef80 100644
--- a/src/jalview/analysis/AlignmentAnnotationUtils.java
+++ b/src/jalview/analysis/AlignmentAnnotationUtils.java
@@ -1,7 +1,26 @@
+/*
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.analysis;
import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.renderer.AnnotationRenderer;
@@ -64,9 +83,16 @@ public class AlignmentAnnotationUtils
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();
@@ -87,8 +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);
}
@@ -130,21 +156,28 @@ public class AlignmentAnnotationUtils
}
}
/*
- * finally add the 'composite group labels' to the appropriate lists,
- * depending on whether the group is identified as visible or hidden
+ * Finally add the 'composite group labels' to the appropriate lists,
+ * depending on whether the group is identified as visible or hidden. Don't
+ * add the same label more than once (there may be many graph groups that
+ * generate it).
*/
for (String calcId : groupLabels.keySet())
{
for (int group : groupLabels.get(calcId).keySet())
{
final List groupLabel = groupLabels.get(calcId).get(group);
+ // don't want to duplicate 'same types in different order'
+ Collections.sort(groupLabel);
if (visibleGraphGroups.get(group))
{
if (!shownTypes.containsKey(calcId))
{
shownTypes.put(calcId, new ArrayList>());
}
- shownTypes.get(calcId).add(groupLabel);
+ if (!shownTypes.get(calcId).contains(groupLabel))
+ {
+ shownTypes.get(calcId).add(groupLabel);
+ }
}
else
{
@@ -152,7 +185,10 @@ public class AlignmentAnnotationUtils
{
hiddenTypes.put(calcId, new ArrayList>());
}
- hiddenTypes.get(calcId).add(groupLabel);
+ if (!hiddenTypes.get(calcId).contains(groupLabel))
+ {
+ hiddenTypes.get(calcId).add(groupLabel);
+ }
}
}
}
@@ -203,4 +239,42 @@ public class AlignmentAnnotationUtils
return (anns == null ? Collections. emptyList()
: Arrays.asList(anns));
}
+
+ /**
+ * replace an existing sequence associated annotation with another, creating
+ * association as necessary.
+ *
+ * @param newAnnot
+ * - annotation row associated with an alignment sequence to be
+ * propagated to its dataset sequence.
+ * @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.getDatasetSequence();
+ while (dsseq.getDatasetSequence() != null)
+ {
+ dsseq = dsseq.getDatasetSequence();
+ }
+ // look for same annotation on dataset and lift this one over
+ List 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();
+ }
+ }
}