X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAnnotationSorter.java;h=83f3adf238bce0f8a64c5476a875330e7666e8a5;hb=a2032664d7eb6954072d43b424e11d219f28df62;hp=2a45b8b2e97577c913f55eaacab41baa26b2b5be;hpb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;p=jalview.git diff --git a/src/jalview/analysis/AnnotationSorter.java b/src/jalview/analysis/AnnotationSorter.java index 2a45b8b..83f3adf 100644 --- a/src/jalview/analysis/AnnotationSorter.java +++ b/src/jalview/analysis/AnnotationSorter.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) - * Copyright (C) 2015 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,6 +20,7 @@ */ package jalview.analysis; +import jalview.api.AlignViewportI; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.SequenceI; @@ -38,7 +39,6 @@ import java.util.Map; */ 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 @@ -50,8 +50,13 @@ 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"), + + /** + * custom is set if user drags to reorder annotations + */ + CUSTOM("Customised"); private String description; @@ -79,27 +84,35 @@ public class AnnotationSorter } } - // the alignment with respect to which annotations are sorted + /* + * the alignment with respect to which annotations are sorted + */ private final AlignmentI alignment; - // user preference for placement of non-sequence annotations + /* + * if true, autocalculated are sorted first, if false, last + */ private boolean showAutocalcAbove; - // working map of sequence index in alignment - private final Map sequenceIndices = new HashMap(); + /* + * working map of sequence index in alignment + */ + private final Map sequenceIndices = new HashMap<>(); + + /* + * if true, sort only repositions auto-calculated annotation (to top or bottom) + */ + private boolean autocalcOnly; /** - * Constructor given an alignment and the location (top or bottom) of - * Consensus and similar. + * Constructor * - * @param alignmentI - * @param showAutocalculatedAbove + * @param av */ - public AnnotationSorter(AlignmentI alignmentI, - boolean showAutocalculatedAbove) + public AnnotationSorter(AlignViewportI av) { - this.alignment = alignmentI; - this.showAutocalcAbove = showAutocalculatedAbove; + this.alignment = av.getAlignment(); + this.showAutocalcAbove = av.isShowAutocalculatedAbove(); } /** @@ -108,7 +121,8 @@ 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)
    • *
*/ @@ -153,6 +167,10 @@ public class AnnotationSorter { return showAutocalcAbove ? 1 : -1; } + if (autocalcOnly) + { + return 0; // don't reorder other annotations + } int sequenceOrder = compareSequences(o1, o2); return sequenceOrder == 0 ? compareLabels(o1, o2) : sequenceOrder; } @@ -169,7 +187,8 @@ 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
    • *
*/ @@ -214,6 +233,10 @@ public class AnnotationSorter { return showAutocalcAbove ? 1 : -1; } + if (autocalcOnly) + { + return 0; // don't reorder other annotations + } int labelOrder = compareLabels(o1, o2); return labelOrder == 0 ? compareSequences(o1, o2) : labelOrder; } @@ -263,50 +286,66 @@ public class AnnotationSorter }; /** - * Sort by the specified ordering of sequence-specific annotations. + * Sorts by the specified ordering. If order is {@code CUSTOM}, meaning + * annotations have been manually ordered by the user, no sort is performed. * - * @param alignmentAnnotations - * @param order + * @param sortBy + * the sort order to apply + * @param autoCalcOnly + * if true, only autocalculated annotations are repositioned (to top + * or bottom), others are left in their current order */ - public void sort(AlignmentAnnotation[] alignmentAnnotations, - SequenceAnnotationOrder order) + public void sort(SequenceAnnotationOrder sortBy, boolean autoCalcOnly) { - if (alignmentAnnotations == null) + if (sortBy == null || sortBy == SequenceAnnotationOrder.CUSTOM) { return; } - // cache 'alignment sequence position' for the annotations - saveSequenceIndices(alignmentAnnotations); - Comparator comparator = getComparator(order); + this.autocalcOnly = autoCalcOnly; - if (alignmentAnnotations != null) + /* + * cache 'alignment sequence positions' if required for sorting + */ + if (sortBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL + || sortBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE) { - synchronized (alignmentAnnotations) - { - Arrays.sort(alignmentAnnotations, comparator); - } + saveSequenceIndices(); + } + + Comparator comparator = getComparator( + sortBy); + + AlignmentAnnotation[] annotations = alignment.getAlignmentAnnotation(); + synchronized (annotations) + { + Arrays.sort(annotations, 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 + * Calculates and saves in a temporary map the position of each annotation's + * associated sequence (if it has one) in the alignment. Faster to do this + * once than for every annotation comparison. */ - private void saveSequenceIndices( - AlignmentAnnotation[] alignmentAnnotations) + private void saveSequenceIndices() { sequenceIndices.clear(); + + Map seqPositions = alignment.getSequencePositions(); + + AlignmentAnnotation[] alignmentAnnotations = alignment + .getAlignmentAnnotation(); for (AlignmentAnnotation ann : alignmentAnnotations) { SequenceI seq = ann.sequenceRef; if (seq != null) { - int index = AlignmentUtils.getSequenceIndex(alignment, seq); - sequenceIndices.put(seq, index); + Integer index = seqPositions.get(seq); + if (index != null) + { + sequenceIndices.put(seq, index); + } } } } @@ -370,7 +409,7 @@ public class AnnotationSorter /** * Comparison based on position of associated sequence (if any) in the - * alignment. Returns zero if either argument is null. + * alignment * * @param o1 * @param o2 @@ -385,8 +424,9 @@ public class AnnotationSorter { return 0; } + /* - * Sort non-sequence-related before or after sequence-related. + * Sort non-sequence-related before or after sequence-related */ if (seq1 == null) { @@ -396,21 +436,20 @@ public class AnnotationSorter { return showAutocalcAbove ? 1 : -1; } - // get sequence index - but note -1 means 'at end' so needs special handling - int index1 = sequenceIndices.get(seq1); - int index2 = sequenceIndices.get(seq2); - if (index1 == index2) - { - return 0; - } - if (index1 == -1) + + /* + * else sort by associated sequence position + */ + Integer index1 = sequenceIndices.get(seq1); + Integer index2 = sequenceIndices.get(seq2); + if (index1 == null) { - return -1; + return index2 == null ? 0 : -1; } - if (index2 == -1) + if (index2 == null) { return 1; } - return Integer.compare(index1, index2); + return Integer.compare(index1.intValue(), index2.intValue()); } }