X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentAnnotationUtils.java;h=f5626cede30458f5f4562cc7af6d411adf6f6a42;hb=8874aa9fd956f7bc248fe15a669a6d8d81d6891b;hp=b5f77fd314c066e28f407097ead14535937a2c32;hpb=195c41c18f6a059b334d063312cd15de6a937ea5;p=jalview.git
diff --git a/src/jalview/analysis/AlignmentAnnotationUtils.java b/src/jalview/analysis/AlignmentAnnotationUtils.java
index b5f77fd..f5626ce 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.analysis;
import jalview.datamodel.AlignmentAnnotation;
@@ -63,9 +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();
@@ -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);
}
@@ -129,21 +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
{
@@ -151,7 +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);
+ }
}
}
}
@@ -196,8 +233,7 @@ public class AlignmentAnnotationUtils
* @param anns
* @return
*/
- public static List asList(
- AlignmentAnnotation[] anns)
+ public static List asList(AlignmentAnnotation[] anns)
{
// TODO use AlignmentAnnotationI instead when it exists
return (anns == null ? Collections. emptyList()