X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=4ebb27f5ee914cbc5e1d2928fb88707bbc0ae96e;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=d41cdd4122d6535b0ef4335aa56a9b17a6c0f668;hpb=9d2408483e451285fd555c3cd6e0273977acbaa7;p=jalview.git diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java index d41cdd4..4ebb27f 100755 --- a/src/jalview/datamodel/AlignmentAnnotation.java +++ b/src/jalview/datamodel/AlignmentAnnotation.java @@ -20,12 +20,6 @@ */ package jalview.datamodel; -import java.util.Locale; - -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; @@ -33,9 +27,14 @@ 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! * @@ -96,6 +95,10 @@ public class AlignmentAnnotation */ private long invalidrnastruc = -2; + private double bitScore; + + private double eValue; + /** * Updates the _rnasecstr field Determines the positions that base pair and * the positions of helices based on secondary structure from a Stockholm file @@ -183,7 +186,8 @@ public class AlignmentAnnotation return rnaSecondaryStructureEquivalent(that, true); } - public boolean rnaSecondaryStructureEquivalent(AlignmentAnnotation that, boolean compareType) + public boolean rnaSecondaryStructureEquivalent(AlignmentAnnotation that, + boolean compareType) { SequenceFeature[] thisSfArray = this.getRnaSecondaryStructure(); SequenceFeature[] thatSfArray = that.getRnaSecondaryStructure(); @@ -196,21 +200,28 @@ public class AlignmentAnnotation return false; } Arrays.sort(thisSfArray, new SFSortByEnd()); // probably already sorted - // like this + // like this Arrays.sort(thatSfArray, new SFSortByEnd()); // probably already sorted - // like this - for (int i=0; i < thisSfArray.length; i++) { + // 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) { + if (compareType) + { + if (thisSf.getType() == null || thatSf.getType() == null) + { + if (thisSf.getType() == null && thatSf.getType() == null) + { continue; - } else { + } + else + { return false; } } - if (! thisSf.getType().equals(thatSf.getType())) { + if (!thisSf.getType().equals(thatSf.getType())) + { return false; } } @@ -374,21 +385,24 @@ public class AlignmentAnnotation // 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' // ambiguous on // its own -- already checked above || annotations[i].secondaryStructure == 'F' - || annotations[i].secondaryStructure == 'G' + // || annotations[i].secondaryStructure == 'G' // || annotations[i].secondaryStructure == 'H' // ambiguous on // its own -- already checked above - || annotations[i].secondaryStructure == 'I' + // || annotations[i].secondaryStructure == 'I' || annotations[i].secondaryStructure == 'J' || annotations[i].secondaryStructure == 'K' || annotations[i].secondaryStructure == 'L' @@ -398,12 +412,12 @@ 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') { @@ -539,12 +553,12 @@ 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 @@ -586,7 +600,7 @@ public class AlignmentAnnotation } return null; } - + /** * Creates a new AlignmentAnnotation object. * @@ -698,7 +712,7 @@ public class AlignmentAnnotation } } } - + /** * Copy constructor creates a new independent annotation row with the same * associated sequenceRef @@ -708,6 +722,17 @@ public class AlignmentAnnotation public AlignmentAnnotation(AlignmentAnnotation annotation) { setAnnotationId(); + updateAlignmentAnnotationFrom(annotation); + } + + /** + * copy attributes and annotation from an existing annotation (used by copy + * constructor). This method does not update the unique annotationId + * + * @param annotation + */ + public void updateAlignmentAnnotationFrom(AlignmentAnnotation annotation) + { this.label = new String(annotation.label); if (annotation.description != null) { @@ -731,6 +756,9 @@ public class AlignmentAnnotation this.scaleColLabel = annotation.scaleColLabel; this.showAllColLabels = annotation.showAllColLabels; this.calcId = annotation.calcId; + this.bitScore = annotation.bitScore; + this.eValue = annotation.eValue; + if (annotation.properties != null) { properties = new HashMap<>(); @@ -962,6 +990,7 @@ public class AlignmentAnnotation * @param seqRef * @param startRes * @param alreadyMapped + * - annotation are at aligned columns */ public void createSequenceMapping(SequenceI seqRef, int startRes, boolean alreadyMapped) @@ -1163,7 +1192,7 @@ public class AlignmentAnnotation { return hasScore || !Double.isNaN(score); } - + /** * Score only annotation * @@ -1194,6 +1223,7 @@ public class AlignmentAnnotation makeVisibleAnnotation(hidden); } + public void setPadGaps(boolean padgaps, char gapchar) { this.padGaps = padgaps; @@ -1653,7 +1683,6 @@ public class AlignmentAnnotation Iterable list, SequenceI seq, String calcId, String label) { - ArrayList aa = new ArrayList<>(); for (AlignmentAnnotation ann : list) { @@ -1698,7 +1727,6 @@ public class AlignmentAnnotation public static Iterable findAnnotation( List list, String calcId) { - List aa = new ArrayList<>(); if (calcId == null) { @@ -1716,4 +1744,42 @@ public class AlignmentAnnotation return aa; } + public double getBitScore() + { + return bitScore; + } + + public void setBitScore(double bitScore) + { + this.bitScore = bitScore; + } + + public double getEValue() + { + return eValue; + } + + public void setEValue(double eValue) + { + this.eValue = eValue; + } + + public static AlignmentAnnotation findFirstAnnotation( + Iterable alignmentAnnotation, String name, + String calcId, boolean autoCalc, SequenceI seqRef, + SequenceGroup groupRef) + { + + for (AlignmentAnnotation annot : alignmentAnnotation) + { + if (annot.autoCalculated == autoCalc && (name.equals(annot.label)) + && (calcId == null || annot.getCalcId().equals(calcId)) + && annot.sequenceRef == seqRef && annot.groupRef == groupRef) + { + return annot; + } + } + return null; + } + }