X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=0f418508abdd229bde007483606a24e5b448a996;hp=c464af2db4fa8d181219e7455c4ad5bf56f6ac82;hb=0ae965fc73680bdc69b06986c060ff17342c4787;hpb=be762d8d9c71a7aa3121e845c45911c7192b7827 diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java index c464af2..0f41850 100755 --- a/src/jalview/datamodel/AlignmentAnnotation.java +++ b/src/jalview/datamodel/AlignmentAnnotation.java @@ -20,18 +20,21 @@ */ package jalview.datamodel; -import jalview.analysis.Rna; -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; import java.util.Iterator; import java.util.List; +import java.util.Locale; import java.util.Map; import java.util.Map.Entry; +import jalview.analysis.Rna; +import jalview.analysis.SecStrConsensus.SimpleBP; +import jalview.analysis.WUSSParseException; + /** * DOCUMENT ME! * @@ -163,6 +166,72 @@ 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; @@ -241,19 +310,6 @@ public class AlignmentAnnotation private boolean isrna; - /* - * (non-Javadoc) - * - * @see java.lang.Object#finalize() - */ - @Override - protected void finalize() throws Throwable - { - sequenceRef = null; - groupRef = null; - super.finalize(); - } - public static int getGraphValueFromString(String string) { if (string.equalsIgnoreCase("BAR_GRAPH")) @@ -306,6 +362,7 @@ 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; @@ -313,27 +370,35 @@ 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 ? + // allow for DSSP extended code: + // https://www.wikidoc.org/index.php/Secondary_structure#The_DSSP_code + // GHITEBS as well as C and X (for missing?) if (annotations[i].secondaryStructure == '(' || annotations[i].secondaryStructure == '[' || annotations[i].secondaryStructure == '<' || annotations[i].secondaryStructure == '{' || annotations[i].secondaryStructure == 'A' - || annotations[i].secondaryStructure == 'B' - || annotations[i].secondaryStructure == 'C' + // || 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 == 'I' + // || annotations[i].secondaryStructure == 'G' + // || annotations[i].secondaryStructure == 'H' // ambiguous on + // its own -- already checked above + // || annotations[i].secondaryStructure == 'I' || annotations[i].secondaryStructure == 'J' || annotations[i].secondaryStructure == 'K' || annotations[i].secondaryStructure == 'L' @@ -343,12 +408,12 @@ public class AlignmentAnnotation || annotations[i].secondaryStructure == 'P' || annotations[i].secondaryStructure == 'Q' || annotations[i].secondaryStructure == 'R' - || annotations[i].secondaryStructure == 'S' - || annotations[i].secondaryStructure == 'T' + // || annotations[i].secondaryStructure == 'S' + // || annotations[i].secondaryStructure == 'T' || annotations[i].secondaryStructure == 'U' || annotations[i].secondaryStructure == 'V' || annotations[i].secondaryStructure == 'W' - || annotations[i].secondaryStructure == 'X' + // || annotations[i].secondaryStructure == 'X' || annotations[i].secondaryStructure == 'Y' || annotations[i].secondaryStructure == 'Z') { @@ -379,7 +444,7 @@ 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' @@ -484,12 +549,12 @@ public class AlignmentAnnotation : annotations[index + offset].displayCharacter == null || annotations[index + offset].displayCharacter - .length() == 0 - ? annotations[index - + offset].secondaryStructure - : annotations[index - + offset].displayCharacter - .charAt(0)); + .length() == 0 + ? annotations[index + + offset].secondaryStructure + : annotations[index + + offset].displayCharacter + .charAt(0)); } @Override @@ -678,7 +743,7 @@ 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()); @@ -714,7 +779,7 @@ 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()) @@ -794,7 +859,7 @@ 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()) { @@ -921,7 +986,7 @@ public class AlignmentAnnotation { return; } - sequenceMapping = new HashMap(); + sequenceMapping = new HashMap<>(); int seqPos; @@ -938,7 +1003,7 @@ public class AlignmentAnnotation seqPos = i + startRes; } - sequenceMapping.put(new Integer(seqPos), annotations[i]); + sequenceMapping.put(Integer.valueOf(seqPos), annotations[i]); } } @@ -977,7 +1042,7 @@ 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) { @@ -1136,7 +1201,7 @@ public class AlignmentAnnotation { return; } - hidden.makeVisibleAnnotation(this); + makeVisibleAnnotation(hidden); } public void setPadGaps(boolean padgaps, char gapchar) @@ -1172,7 +1237,7 @@ public class AlignmentAnnotation { if (seqname && this.sequenceRef != null) { - int i = description.toLowerCase().indexOf(""); + int i = description.toLowerCase(Locale.ROOT).indexOf(""); if (i > -1) { // move the html tag to before the sequence reference. @@ -1202,7 +1267,7 @@ 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 @@ -1248,7 +1313,7 @@ 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) @@ -1301,7 +1366,7 @@ 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()) { @@ -1359,7 +1424,7 @@ public class AlignmentAnnotation { if (properties == null) { - properties = new HashMap(); + properties = new HashMap<>(); } properties.put(property, value); } @@ -1484,4 +1549,181 @@ 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) + { + + ArrayList aa = new ArrayList<>(); + for (AlignmentAnnotation ann : list) + { + if ((calcId == null || (ann.getCalcId() != null + && ann.getCalcId().equals(calcId))) + && (seq == null || (ann.sequenceRef != null + && ann.sequenceRef == seq)) + && (label == null + || (ann.label != null && ann.label.equals(label)))) + { + aa.add(ann); + } + } + return aa; + } + + /** + * Answer true if any annotation matches the calcId passed in (if not null). + * + * @param list + * annotation to search + * @param calcId + * @return + */ + public static boolean hasAnnotation(List list, + String calcId) + { + + if (calcId != null && !"".equals(calcId)) + { + for (AlignmentAnnotation a : list) + { + if (a.getCalcId() == calcId) + { + return true; + } + } + } + return false; + } + + public static Iterable findAnnotation( + List list, String calcId) + { + + List aa = new ArrayList<>(); + if (calcId == null) + { + return aa; + } + for (AlignmentAnnotation a : list) + { + + if (a.getCalcId() == calcId || (a.getCalcId() != null + && calcId != null && a.getCalcId().equals(calcId))) + { + aa.add(a); + } + } + return aa; + } + }