X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=6ac5da8b1d3ebc62786694083ade1ed03fbe974f;hb=d5477e299373c07a2b1f92421dcf454b0fe40b56;hp=d6bfd93b41a26173fedc826bd408d1feae4dcdd6;hpb=bd6ce8f5f9fc8e5bc8a6188d15987ce0ffd2c1ee;p=jalview.git diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java index d6bfd93..6ac5da8 100755 --- a/src/jalview/datamodel/AlignmentAnnotation.java +++ b/src/jalview/datamodel/AlignmentAnnotation.java @@ -25,6 +25,7 @@ import jalview.analysis.SecStrConsensus.SimpleBP; import jalview.analysis.WUSSParseException; import java.util.ArrayList; +import java.util.Arrays; import java.util.Collection; import java.util.Collections; import java.util.HashMap; @@ -164,6 +165,64 @@ public class AlignmentAnnotation } /** + * Get the RNA Secondary Structure SequenceFeature Array if present + */ + public SequenceFeature[] getRnaSecondaryStructure() + { + return this._rnasecstr; + } + + /** + * Check the RNA Secondary Structure is equivalent to one in given + * AlignmentAnnotation param + */ + public boolean rnaSecondaryStructureEquivalent(AlignmentAnnotation that) + { + return rnaSecondaryStructureEquivalent(that, true); + } + + public boolean rnaSecondaryStructureEquivalent(AlignmentAnnotation that, boolean compareType) + { + SequenceFeature[] thisSfArray = this.getRnaSecondaryStructure(); + SequenceFeature[] thatSfArray = that.getRnaSecondaryStructure(); + if (thisSfArray == null || thatSfArray == null) + { + return thisSfArray == null && thatSfArray == null; + } + if (thisSfArray.length != thatSfArray.length) + { + return false; + } + Arrays.sort(thisSfArray, new SFSortByEnd()); // probably already sorted + // like this + Arrays.sort(thatSfArray, new SFSortByEnd()); // probably already sorted + // like this + for (int i=0; i < thisSfArray.length; i++) { + SequenceFeature thisSf = thisSfArray[i]; + SequenceFeature thatSf = thatSfArray[i]; + if (compareType) { + if (thisSf.getType() == null || thatSf.getType() == null) { + if (thisSf.getType() == null && thatSf.getType() == null) { + continue; + } else { + return false; + } + } + if (! thisSf.getType().equals(thatSf.getType())) { + return false; + } + } + if (!(thisSf.getBegin() == thatSf.getBegin() + && thisSf.getEnd() == thatSf.getEnd())) + { + return false; + } + } + return true; + + } + + /** * map of positions in the associated annotation */ private Map sequenceMapping; @@ -294,6 +353,7 @@ public class AlignmentAnnotation char firstChar = 0; for (int i = 0; i < annotations.length; i++) { + // DEBUG System.out.println(i + ": " + annotations[i]); if (annotations[i] == null) { continue; @@ -301,12 +361,15 @@ public class AlignmentAnnotation if (annotations[i].secondaryStructure == 'H' || annotations[i].secondaryStructure == 'E') { + // DEBUG System.out.println( "/H|E/ '" + + // annotations[i].secondaryStructure + "'"); hasIcons |= true; } else // Check for RNA secondary structure { - // System.out.println(annotations[i].secondaryStructure); + // DEBUG System.out.println( "/else/ '" + + // annotations[i].secondaryStructure + "'"); // TODO: 2.8.2 should this ss symbol validation check be a function in // RNA/ResidueProperties ? if (annotations[i].secondaryStructure == '(' @@ -317,10 +380,12 @@ public class AlignmentAnnotation || annotations[i].secondaryStructure == 'B' || annotations[i].secondaryStructure == 'C' || annotations[i].secondaryStructure == 'D' - || annotations[i].secondaryStructure == 'E' + // || annotations[i].secondaryStructure == 'E' // ambiguous on + // its own -- already checked above || annotations[i].secondaryStructure == 'F' || annotations[i].secondaryStructure == 'G' - || annotations[i].secondaryStructure == 'H' + // || annotations[i].secondaryStructure == 'H' // ambiguous on + // its own -- already checked above || annotations[i].secondaryStructure == 'I' || annotations[i].secondaryStructure == 'J' || annotations[i].secondaryStructure == 'K' @@ -367,7 +432,7 @@ public class AlignmentAnnotation // && // annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure firstChar != ' ' && firstChar != '$' && firstChar != 0xCE - && firstChar != '(' && firstChar != '[' && firstChar != '>' + && firstChar != '(' && firstChar != '[' && firstChar != '<' && firstChar != '{' && firstChar != 'A' && firstChar != 'B' && firstChar != 'C' && firstChar != 'D' && firstChar != 'E' && firstChar != 'F' && firstChar != 'G' && firstChar != 'H' @@ -519,7 +584,7 @@ public class AlignmentAnnotation } return null; } - + /** * Creates a new AlignmentAnnotation object. * @@ -631,7 +696,7 @@ public class AlignmentAnnotation } } } - + /** * Copy constructor creates a new independent annotation row with the same * associated sequenceRef @@ -895,6 +960,7 @@ public class AlignmentAnnotation * @param seqRef * @param startRes * @param alreadyMapped + * - annotation are at aligned columns */ public void createSequenceMapping(SequenceI seqRef, int startRes, boolean alreadyMapped) @@ -926,7 +992,7 @@ public class AlignmentAnnotation seqPos = i + startRes; } - sequenceMapping.put(new Integer(seqPos), annotations[i]); + sequenceMapping.put(Integer.valueOf(seqPos), annotations[i]); } } @@ -965,7 +1031,7 @@ public class AlignmentAnnotation { for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++) { - index = new Integer(a); + index = Integer.valueOf(a); Annotation annot = sequenceMapping.get(index); if (annot != null) { @@ -1096,7 +1162,7 @@ public class AlignmentAnnotation { return hasScore || !Double.isNaN(score); } - + /** * Score only annotation * @@ -1124,9 +1190,10 @@ public class AlignmentAnnotation { return; } - hidden.makeVisibleAnnotation(this); + makeVisibleAnnotation(hidden); } + public void setPadGaps(boolean padgaps, char gapchar) { this.padGaps = padgaps; @@ -1473,11 +1540,120 @@ public class AlignmentAnnotation return graphMin < graphMax; } + /** + * delete any columns in alignmentAnnotation that are hidden (including + * sequence associated annotation). + * + * @param hiddenColumns + * the set of hidden columns + */ + public void makeVisibleAnnotation(HiddenColumns hiddenColumns) + { + if (annotations != null) + { + makeVisibleAnnotation(0, annotations.length, hiddenColumns); + } + } + + /** + * delete any columns in alignmentAnnotation that are hidden (including + * sequence associated annotation). + * + * @param start + * remove any annotation to the right of this column + * @param end + * remove any annotation to the left of this column + * @param hiddenColumns + * the set of hidden columns + */ + public void makeVisibleAnnotation(int start, int end, + HiddenColumns hiddenColumns) + { + if (annotations != null) + { + if (hiddenColumns.hasHiddenColumns()) + { + removeHiddenAnnotation(start, end, hiddenColumns); + } + else + { + restrict(start, end); + } + } + } + + /** + * The actual implementation of deleting hidden annotation columns + * + * @param start + * remove any annotation to the right of this column + * @param end + * remove any annotation to the left of this column + * @param hiddenColumns + * the set of hidden columns + */ + private void removeHiddenAnnotation(int start, int end, + HiddenColumns hiddenColumns) + { + // mangle the alignmentAnnotation annotation array + ArrayList annels = new ArrayList<>(); + Annotation[] els = null; + + int w = 0; + + Iterator blocks = hiddenColumns.getVisContigsIterator(start, + end + 1, false); + + int copylength; + int annotationLength; + while (blocks.hasNext()) + { + int[] block = blocks.next(); + annotationLength = block[1] - block[0] + 1; + + if (blocks.hasNext()) + { + // copy just the visible segment of the annotation row + copylength = annotationLength; + } + else + { + if (annotationLength + block[0] <= annotations.length) + { + // copy just the visible segment of the annotation row + copylength = annotationLength; + } + else + { + // copy to the end of the annotation row + copylength = annotations.length - block[0]; + } + } + + els = new Annotation[annotationLength]; + annels.add(els); + System.arraycopy(annotations, block[0], els, 0, copylength); + w += annotationLength; + } + + if (w != 0) + { + annotations = new Annotation[w]; + + w = 0; + for (Annotation[] chnk : annels) + { + System.arraycopy(chnk, 0, annotations, w, chnk.length); + w += chnk.length; + } + } + } + public static Iterable findAnnotations( Iterable list, SequenceI seq, String calcId, String label) { - List aa = new ArrayList<>(); + ArrayList aa = new ArrayList<>(); for (AlignmentAnnotation ann : list) { if ((calcId == null || (ann.getCalcId() != null @@ -1537,4 +1713,5 @@ public class AlignmentAnnotation } return aa; } + }