X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAnnotationSorter.java;h=711e8c9c8600350871b63c7ef460a58f07966941;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=fa9c1a83f82ca41bfeda16ca30d5de61f758f3c3;hpb=eaf9092bfa74b5162589c8775f68a19dd79dbb1d;p=jalview.git
diff --git a/src/jalview/analysis/AnnotationSorter.java b/src/jalview/analysis/AnnotationSorter.java
index fa9c1a8..711e8c9 100644
--- a/src/jalview/analysis/AnnotationSorter.java
+++ b/src/jalview/analysis/AnnotationSorter.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;
@@ -6,6 +26,8 @@ import jalview.datamodel.SequenceI;
import java.util.Arrays;
import java.util.Comparator;
+import java.util.HashMap;
+import java.util.Map;
/**
* A helper class to sort all annotations associated with an alignment in
@@ -17,15 +39,55 @@ import java.util.Comparator;
public class AnnotationSorter
{
+ /**
+ * enum for annotation sort options. The text description is used in the
+ * Preferences drop-down options. The enum name is saved in the preferences
+ * file.
+ *
+ * @author gmcarstairs
+ *
+ */
public enum SequenceAnnotationOrder
{
- SEQUENCE_AND_LABEL, LABEL_AND_SEQUENCE, NONE
+ // Text descriptions surface in the Preferences Sort by... options
+ SEQUENCE_AND_LABEL("Sequence"), LABEL_AND_SEQUENCE("Label"), NONE(
+ "No sort");
+
+ private String description;
+
+ private SequenceAnnotationOrder(String s)
+ {
+ description = s;
+ }
+
+ @Override
+ public String toString()
+ {
+ return description;
+ }
+
+ public static SequenceAnnotationOrder forDescription(String d)
+ {
+ for (SequenceAnnotationOrder order : values())
+ {
+ if (order.toString().equals(d))
+ {
+ return order;
+ }
+ }
+ return null;
+ }
}
-
+
+ // the alignment with respect to which annotations are sorted
private final AlignmentI alignment;
+ // user preference for placement of non-sequence annotations
private boolean showAutocalcAbove;
+ // working map of sequence index in alignment
+ private final Map sequenceIndices = new HashMap();
+
/**
* Constructor given an alignment and the location (top or bottom) of
* Consensus and similar.
@@ -68,17 +130,38 @@ public class AnnotationSorter
return 1;
}
+ // TODO how to treat sequence-related autocalculated annotation
+ boolean o1auto = o1.autoCalculated && o1.sequenceRef == null;
+ boolean o2auto = o2.autoCalculated && o2.sequenceRef == null;
/*
* Ignore label (keep existing ordering) for
* Conservation/Quality/Consensus etc
*/
- if (o1.sequenceRef == null && o2.sequenceRef == null)
+ if (o1auto && o2auto)
{
return 0;
}
+
+ /*
+ * Sort autocalculated before or after sequence-related.
+ */
+ if (o1auto)
+ {
+ return showAutocalcAbove ? -1 : 1;
+ }
+ if (o2auto)
+ {
+ return showAutocalcAbove ? 1 : -1;
+ }
int sequenceOrder = compareSequences(o1, o2);
return sequenceOrder == 0 ? compareLabels(o1, o2) : sequenceOrder;
}
+
+ @Override
+ public String toString()
+ {
+ return "Sort by sequence and label";
+ }
};
/**
@@ -108,57 +191,77 @@ public class AnnotationSorter
return 1;
}
+ // TODO how to treat sequence-related autocalculated annotation
+ boolean o1auto = o1.autoCalculated && o1.sequenceRef == null;
+ boolean o2auto = o2.autoCalculated && o2.sequenceRef == null;
/*
* Ignore label (keep existing ordering) for
* Conservation/Quality/Consensus etc
*/
- if (o1.sequenceRef == null && o2.sequenceRef == null)
+ if (o1auto && o2auto)
{
return 0;
}
/*
- * Sort non-sequence-related before or after sequence-related.
+ * Sort autocalculated before or after sequence-related.
*/
- if (o1.sequenceRef == null)
+ if (o1auto)
{
return showAutocalcAbove ? -1 : 1;
}
- if (o2.sequenceRef == null)
+ if (o2auto)
{
return showAutocalcAbove ? 1 : -1;
}
int labelOrder = compareLabels(o1, o2);
return labelOrder == 0 ? compareSequences(o1, o2) : labelOrder;
}
+
+ @Override
+ public String toString()
+ {
+ return "Sort by label and sequence";
+ }
};
/**
- * noSort leaves sort order unchanged, within sequence- and
- * non-sequence-related annotations, but may switch the ordering of these
- * groups. Note this is guaranteed (at least in Java 7) as Arrays.sort() is
- * guaranteed to be 'stable' (not change ordering of equal items).
+ * noSort leaves sort order unchanged, within sequence- and autocalculated
+ * annotations, but may switch the ordering of these groups. Note this is
+ * guaranteed (at least in Java 7) as Arrays.sort() is guaranteed to be
+ * 'stable' (not change ordering of equal items).
*/
private Comparator noSort = new Comparator()
{
@Override
public int compare(AlignmentAnnotation o1, AlignmentAnnotation o2)
{
+ // TODO how to treat sequence-related autocalculated annotation
+ boolean o1auto = o1.autoCalculated && o1.sequenceRef == null;
+ boolean o2auto = o2.autoCalculated && o2.sequenceRef == null;
+ // TODO skip this test to allow customised ordering of all annotations
+ // - needs a third option: place autocalculated first / last / none
if (o1 != null && o2 != null)
{
- if (o1.sequenceRef == null && o2.sequenceRef != null)
+ if (o1auto && !o2auto)
{
return showAutocalcAbove ? -1 : 1;
}
- if (o1.sequenceRef != null && o2.sequenceRef == null)
+ if (!o1auto && o2auto)
{
return showAutocalcAbove ? 1 : -1;
}
}
return 0;
}
+
+ @Override
+ public String toString()
+ {
+ return "No sort";
+ }
};
-
+
/**
* Sort by the specified ordering of sequence-specific annotations.
*
@@ -168,16 +271,42 @@ public class AnnotationSorter
public void sort(AlignmentAnnotation[] alignmentAnnotations,
SequenceAnnotationOrder order)
{
- if (order != SequenceAnnotationOrder.NONE)
+ if (alignmentAnnotations == null)
{
- Comparator comparator = getComparator(order);
+ return;
+ }
+ // cache 'alignment sequence position' for the annotations
+ saveSequenceIndices(alignmentAnnotations);
- if (alignmentAnnotations != null)
+ Comparator comparator = getComparator(order);
+
+ if (alignmentAnnotations != null)
+ {
+ synchronized (alignmentAnnotations)
{
- synchronized (alignmentAnnotations)
- {
- Arrays.sort(alignmentAnnotations, comparator);
- }
+ Arrays.sort(alignmentAnnotations, comparator);
+ }
+ }
+ }
+
+ /**
+ * Calculate and save in a temporary map the position of each annotation's
+ * sequence (if it has one) in the alignment. Faster to do this once than for
+ * every annotation comparison.
+ *
+ * @param alignmentAnnotations
+ */
+ private void saveSequenceIndices(
+ AlignmentAnnotation[] alignmentAnnotations)
+ {
+ sequenceIndices.clear();
+ for (AlignmentAnnotation ann : alignmentAnnotations)
+ {
+ SequenceI seq = ann.sequenceRef;
+ if (seq != null)
+ {
+ int index = AlignmentUtils.getSequenceIndex(alignment, seq);
+ sequenceIndices.put(seq, index);
}
}
}
@@ -268,8 +397,8 @@ public class AnnotationSorter
return showAutocalcAbove ? 1 : -1;
}
// get sequence index - but note -1 means 'at end' so needs special handling
- int index1 = AlignmentUtils.getSequenceIndex(alignment, seq1);
- int index2 = AlignmentUtils.getSequenceIndex(alignment, seq2);
+ int index1 = sequenceIndices.get(seq1);
+ int index2 = sequenceIndices.get(seq2);
if (index1 == index2)
{
return 0;