X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fanalysis%2FAnnotationSorter.java;h=92ed9bec374645afb0f6099c73e4688e7f6f852a;hb=4abe263f327773456c984373a8387e4d8c3be5a9;hp=28fa1f8a2667bb42a37b0f8e6e75bf32e90de2c1;hpb=7c5e7c1c51a48eab1b217a221df82748c35b76b1;p=jalview.git
diff --git a/src/jalview/analysis/AnnotationSorter.java b/src/jalview/analysis/AnnotationSorter.java
index 28fa1f8..92ed9be 100644
--- a/src/jalview/analysis/AnnotationSorter.java
+++ b/src/jalview/analysis/AnnotationSorter.java
@@ -1,11 +1,35 @@
+/*
+ * 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 java.util.Locale;
+
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
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
@@ -28,8 +52,8 @@ public class AnnotationSorter
public enum SequenceAnnotationOrder
{
// Text descriptions surface in the Preferences Sort by... options
- SEQUENCE_AND_LABEL("Sequence"), LABEL_AND_SEQUENCE("Label"), NONE(
- "No sort");
+ SEQUENCE_AND_LABEL("Sequence"), LABEL_AND_SEQUENCE("Label"),
+ NONE("No sort");
private String description;
@@ -44,7 +68,8 @@ public class AnnotationSorter
return description;
}
- public static SequenceAnnotationOrder forDescription(String d) {
+ public static SequenceAnnotationOrder forDescription(String d)
+ {
for (SequenceAnnotationOrder order : values())
{
if (order.toString().equals(d))
@@ -56,10 +81,15 @@ public class AnnotationSorter
}
}
+ // 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.
@@ -80,7 +110,8 @@ public class AnnotationSorter
*
* - annotations with a reference to a sequence in the alignment are sorted
* on sequence ordering
- * - other annotations go 'at the end', with their mutual order unchanged
+ * - other annotations go 'at the end', with their mutual order
+ * unchanged
* - within the same sequence ref, sort by label (non-case-sensitive)
*
*/
@@ -102,17 +133,38 @@ 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";
+ }
};
/**
@@ -120,7 +172,8 @@ public class AnnotationSorter
*
* - annotations with a reference to a sequence in the alignment are sorted
* on label (non-case-sensitive)
- * - other annotations go 'at the end', with their mutual order unchanged
+ * - other annotations go 'at the end', with their mutual order
+ * unchanged
* - within the same label, sort by order of the related sequences
*
*/
@@ -142,55 +195,75 @@ 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 super AlignmentAnnotation> 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";
+ }
};
/**
@@ -202,7 +275,15 @@ public class AnnotationSorter
public void sort(AlignmentAnnotation[] alignmentAnnotations,
SequenceAnnotationOrder order)
{
- Comparator super AlignmentAnnotation> comparator = getComparator(order);
+ if (alignmentAnnotations == null)
+ {
+ return;
+ }
+ // cache 'alignment sequence position' for the annotations
+ saveSequenceIndices(alignmentAnnotations);
+
+ Comparator super AlignmentAnnotation> comparator = getComparator(
+ order);
if (alignmentAnnotations != null)
{
@@ -214,6 +295,28 @@ public class AnnotationSorter
}
/**
+ * 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);
+ }
+ }
+ }
+
+ /**
* Get the comparator for the specified sort order.
*
* @param order
@@ -267,7 +370,8 @@ public class AnnotationSorter
{
return 1;
}
- return label1.toUpperCase().compareTo(label2.toUpperCase());
+ return label1.toUpperCase(Locale.ROOT)
+ .compareTo(label2.toUpperCase(Locale.ROOT));
}
/**
@@ -299,8 +403,8 @@ 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;