X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=ee9389c04dc6697b89a8f2857e3948d4c3eb6ac1;hb=bab4b08733a9543bdce5c0b9d1c32ca7d18ad9e3;hp=ffc31050f092dcf99163e12e043ae772d514f807;hpb=06f7fc9313488587d9c0158b830ff66a68336ce3;p=jalview.git diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java index ffc3105..ee9389c 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' @@ -666,7 +731,7 @@ public class AlignmentAnnotation this.calcId = annotation.calcId; if (annotation.properties != null) { - properties = new HashMap(); + properties = new HashMap<>(); for (Map.Entry val : annotation.properties.entrySet()) { properties.put(val.getKey(), val.getValue()); @@ -702,7 +767,7 @@ public class AlignmentAnnotation if (annotation.sequenceMapping != null) { Integer p = null; - sequenceMapping = new HashMap(); + sequenceMapping = new HashMap<>(); Iterator pos = annotation.sequenceMapping.keySet() .iterator(); while (pos.hasNext()) @@ -782,7 +847,7 @@ public class AlignmentAnnotation int epos = sequenceRef.findPosition(endRes); if (sequenceMapping != null) { - Map newmapping = new HashMap(); + Map newmapping = new HashMap<>(); Iterator e = sequenceMapping.keySet().iterator(); while (e.hasNext()) { @@ -909,7 +974,7 @@ public class AlignmentAnnotation { return; } - sequenceMapping = new HashMap(); + sequenceMapping = new HashMap<>(); int seqPos; @@ -1124,7 +1189,7 @@ public class AlignmentAnnotation { return; } - hidden.makeVisibleAnnotation(this); + makeVisibleAnnotation(hidden); } public void setPadGaps(boolean padgaps, char gapchar) @@ -1190,7 +1255,7 @@ public class AlignmentAnnotation /** * properties associated with the calcId */ - protected Map properties = new HashMap(); + protected Map properties = new HashMap<>(); /** * base colour for line graphs. If null, will be set automatically by @@ -1236,7 +1301,7 @@ public class AlignmentAnnotation : false; // TODO build a better annotation element map and get rid of annotations[] - Map mapForsq = new HashMap(); + Map mapForsq = new HashMap<>(); if (sequenceMapping != null) { if (sp2sq != null) @@ -1289,7 +1354,7 @@ public class AlignmentAnnotation if (mapping != null) { Map old = sequenceMapping; - Map remap = new HashMap(); + Map remap = new HashMap<>(); int index = -1; for (int mp[] : mapping.values()) { @@ -1347,7 +1412,7 @@ public class AlignmentAnnotation { if (properties == null) { - properties = new HashMap(); + properties = new HashMap<>(); } properties.put(property, value); } @@ -1473,6 +1538,115 @@ 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) @@ -1530,11 +1704,14 @@ public class AlignmentAnnotation } for (AlignmentAnnotation a : list) { - if (calcId.equals(a.getCalcId())) + + if (a.getCalcId() == calcId || (a.getCalcId() != null + && calcId != null && a.getCalcId().equals(calcId))) { aa.add(a); } } return aa; } + }