X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=6bbd56614559c0bea3381156f7dba04888cf7316;hb=3d0101179759ef157b088ea135423cd909512d9f;hp=95141e60c182a7c12be392cecb9dfdcc0f9d0af0;hpb=57dd16688caa6dacaeaf465bab3ee8b6126e1a51;p=jalview.git diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java index 95141e6..6bbd566 100755 --- a/src/jalview/datamodel/AlignmentAnnotation.java +++ b/src/jalview/datamodel/AlignmentAnnotation.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) - * 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. * @@ -24,11 +24,11 @@ import jalview.analysis.Rna; import jalview.analysis.SecStrConsensus.SimpleBP; import jalview.analysis.WUSSParseException; -import java.util.ArrayList; import java.util.Collection; import java.util.Collections; import java.util.HashMap; import java.util.Iterator; +import java.util.List; import java.util.Map; import java.util.Map.Entry; @@ -79,7 +79,7 @@ public class AlignmentAnnotation /** Array of annotations placed in the current coordinate system */ public Annotation[] annotations; - public ArrayList bps = null; + public List bps = null; /** * RNA secondary structure contact positions @@ -102,8 +102,8 @@ public class AlignmentAnnotation { try { - _rnasecstr = Rna.GetBasePairs(RNAannot); - bps = Rna.GetModeleBP(RNAannot); + bps = Rna.getModeleBP(RNAannot); + _rnasecstr = Rna.getBasePairs(bps); invalidrnastruc = -1; } catch (WUSSParseException px) { @@ -170,10 +170,14 @@ public class AlignmentAnnotation */ private Map sequenceMapping; - /** DOCUMENT ME!! */ + /** + * lower range for quantitative data + */ public float graphMin; - /** DOCUMENT ME!! */ + /** + * Upper range for quantitative data + */ public float graphMax; /** @@ -245,6 +249,7 @@ public class AlignmentAnnotation * * @see java.lang.Object#finalize() */ + @Override protected void finalize() throws Throwable { sequenceRef = null; @@ -271,7 +276,7 @@ public class AlignmentAnnotation // JBPNote: what does this do ? public void ConcenStru(CharSequence RNAannot) throws WUSSParseException { - bps = Rna.GetModeleBP(RNAannot); + bps = Rna.getModeleBP(RNAannot); } /** @@ -374,49 +379,25 @@ public class AlignmentAnnotation firstChar = annotations[i].displayCharacter.charAt(0); // check to see if it looks like a sequence or is secondary structure // labelling. - if (annotations[i].secondaryStructure != ' ' - && !hasIcons - && - // Uncomment to only catch case where - // displayCharacter==secondary - // Structure - // to correctly redisplay SS annotation imported from Stockholm, - // exported to JalviewXML and read back in again. - // && - // annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure - firstChar != ' ' - && firstChar != '$' - && firstChar != 0xCE - && firstChar != '(' - && firstChar != '[' - && firstChar != '>' - && firstChar != '{' - && firstChar != 'A' - && firstChar != 'B' - && firstChar != 'C' - && firstChar != 'D' - && firstChar != 'E' - && firstChar != 'F' - && firstChar != 'G' - && firstChar != 'H' - && firstChar != 'I' - && firstChar != 'J' - && firstChar != 'K' - && firstChar != 'L' - && firstChar != 'M' - && firstChar != 'N' - && firstChar != 'O' - && firstChar != 'P' - && firstChar != 'Q' - && firstChar != 'R' - && firstChar != 'S' - && firstChar != 'T' - && firstChar != 'U' - && firstChar != 'V' - && firstChar != 'W' - && firstChar != 'X' - && firstChar != 'Y' - && firstChar != 'Z' + if (annotations[i].secondaryStructure != ' ' && !hasIcons && + // Uncomment to only catch case where + // displayCharacter==secondary + // Structure + // to correctly redisplay SS annotation imported from Stockholm, + // exported to JalviewXML and read back in again. + // && + // annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure + firstChar != ' ' && firstChar != '$' && firstChar != 0xCE + && firstChar != '(' && firstChar != '[' && firstChar != '>' + && firstChar != '{' && firstChar != 'A' && firstChar != 'B' + && firstChar != 'C' && firstChar != 'D' && firstChar != 'E' + && firstChar != 'F' && firstChar != 'G' && firstChar != 'H' + && firstChar != 'I' && firstChar != 'J' && firstChar != 'K' + && firstChar != 'L' && firstChar != 'M' && firstChar != 'N' + && firstChar != 'O' && firstChar != 'P' && firstChar != 'Q' + && firstChar != 'R' && firstChar != 'S' && firstChar != 'T' + && firstChar != 'U' && firstChar != 'V' && firstChar != 'W' + && firstChar != 'X' && firstChar != 'Y' && firstChar != 'Z' && firstChar != '-' && firstChar < jalview.schemes.ResidueProperties.aaIndex.length) { @@ -484,7 +465,7 @@ public class AlignmentAnnotation this(0, annotations.length); } - public AnnotCharSequence(int start, int end) + AnnotCharSequence(int start, int end) { offset = start; max = end; @@ -507,12 +488,17 @@ public class AlignmentAnnotation { return ((index + offset < 0) || (index + offset) >= max || annotations[index + offset] == null - || (annotations[index + offset].secondaryStructure <= ' ') ? ' ' - : annotations[index + offset].displayCharacter == null - || annotations[index + offset].displayCharacter - .length() == 0 ? annotations[index + offset].secondaryStructure - : annotations[index + offset].displayCharacter - .charAt(0)); + || (annotations[index + offset].secondaryStructure <= ' ') + ? ' ' + : annotations[index + offset].displayCharacter == null + || annotations[index + + offset].displayCharacter + .length() == 0 + ? annotations[index + + offset].secondaryStructure + : annotations[index + + offset].displayCharacter + .charAt(0)); } @Override @@ -523,10 +509,15 @@ public class AlignmentAnnotation for (int i = offset; i < mx; i++) { - string[i] = (annotations[i] == null || (annotations[i].secondaryStructure <= 32)) ? ' ' - : (annotations[i].displayCharacter == null - || annotations[i].displayCharacter.length() == 0 ? annotations[i].secondaryStructure - : annotations[i].displayCharacter.charAt(0)); + string[i] = (annotations[i] == null + || (annotations[i].secondaryStructure <= 32)) + ? ' ' + : (annotations[i].displayCharacter == null + || annotations[i].displayCharacter + .length() == 0 + ? annotations[i].secondaryStructure + : annotations[i].displayCharacter + .charAt(0)); } return new String(string); } @@ -592,6 +583,7 @@ public class AlignmentAnnotation if (annotations == null) { visible = false; // try to prevent renderer from displaying. + invalidrnastruc = -1; return; // this is a non-annotation row annotation - ie a sequence score. } @@ -801,8 +793,8 @@ public class AlignmentAnnotation Annotation[] temp = new Annotation[endRes - startRes + 1]; if (startRes < annotations.length) { - System.arraycopy(annotations, startRes, temp, 0, endRes - startRes - + 1); + System.arraycopy(annotations, startRes, temp, 0, + endRes - startRes + 1); } if (sequenceRef != null) { @@ -861,6 +853,10 @@ public class AlignmentAnnotation @Override public String toString() { + if (annotations == null) + { + return ""; + } StringBuilder buffer = new StringBuilder(256); for (int i = 0; i < annotations.length; i++) @@ -1018,8 +1014,8 @@ public class AlignmentAnnotation { if (i + 1 < iSize) { - System.arraycopy(annotations, i + 1, annotations, i, iSize - i - - 1); + System.arraycopy(annotations, i + 1, annotations, i, + iSize - i - 1); } iSize--; } @@ -1051,14 +1047,16 @@ public class AlignmentAnnotation { if (sequenceRef != null) { - boolean rIsDs = sequenceRef.getDatasetSequence() == null, tIsDs = sequenceI - .getDatasetSequence() == null; + boolean rIsDs = sequenceRef.getDatasetSequence() == null, + tIsDs = sequenceI.getDatasetSequence() == null; if (sequenceRef != sequenceI - && (rIsDs && !tIsDs && sequenceRef != sequenceI - .getDatasetSequence()) - && (!rIsDs && tIsDs && sequenceRef.getDatasetSequence() != sequenceI) - && (!rIsDs && !tIsDs && sequenceRef.getDatasetSequence() != sequenceI - .getDatasetSequence()) + && (rIsDs && !tIsDs + && sequenceRef != sequenceI.getDatasetSequence()) + && (!rIsDs && tIsDs + && sequenceRef.getDatasetSequence() != sequenceI) + && (!rIsDs && !tIsDs + && sequenceRef.getDatasetSequence() != sequenceI + .getDatasetSequence()) && !sequenceRef.equals(sequenceI)) { // if sequenceRef isn't intersecting with sequenceI @@ -1140,14 +1138,14 @@ public class AlignmentAnnotation * @param colSel */ public AlignmentAnnotation(AlignmentAnnotation alignmentAnnotation, - ColumnSelection colSel) + HiddenColumns hidden) { this(alignmentAnnotation); if (annotations == null) { return; } - colSel.makeVisibleAnnotation(this); + hidden.makeVisibleAnnotation(this); } public void setPadGaps(boolean padgaps, char gapchar) @@ -1253,8 +1251,10 @@ public class AlignmentAnnotation throw new Error( "liftOver currently not implemented for transfer of annotation between different types of seqeunce"); } - boolean mapIsTo = (sp2sq != null) ? (sp2sq.getTo() == sq || sp2sq - .getTo() == sq.getDatasetSequence()) : false; + boolean mapIsTo = (sp2sq != null) + ? (sp2sq.getTo() == sq + || sp2sq.getTo() == sq.getDatasetSequence()) + : false; // TODO build a better annotation element map and get rid of annotations[] Map mapForsq = new HashMap(); @@ -1264,9 +1264,9 @@ public class AlignmentAnnotation { for (Entry ie : sequenceMapping.entrySet()) { - Integer mpos = Integer.valueOf(mapIsTo ? sp2sq - .getMappedPosition(ie.getKey()) : sp2sq.getPosition(ie - .getKey())); + Integer mpos = Integer + .valueOf(mapIsTo ? sp2sq.getMappedPosition(ie.getKey()) + : sp2sq.getPosition(ie.getKey())); if (mpos >= sq.getStart() && mpos <= sq.getEnd()) { mapForsq.put(mpos, ie.getValue()); @@ -1304,15 +1304,15 @@ public class AlignmentAnnotation * @note caller should add the remapped annotation to newref if they have not * already */ - public void remap(SequenceI newref, int[][] mapping, int from, int to, - int idxoffset) + public void remap(SequenceI newref, HashMap mapping, + int from, int to, int idxoffset) { if (mapping != null) { Map old = sequenceMapping; Map remap = new HashMap(); int index = -1; - for (int mp[] : mapping) + for (int mp[] : mapping.values()) { if (index++ < 0) { @@ -1409,8 +1409,88 @@ public class AlignmentAnnotation this.annotationId = ANNOTATION_ID_PREFIX + Long.toString(nextId()); } + /** + * Returns the match for the last unmatched opening RNA helix pair symbol + * preceding the given column, or '(' if nothing found to match. + * + * @param column + * @return + */ + public String getDefaultRnaHelixSymbol(int column) + { + String result = "("; + if (annotations == null) + { + return result; + } + + /* + * for each preceding column, if it contains an open bracket, + * count whether it is still unmatched at column, if so return its pair + * (likely faster than the fancy alternative using stacks) + */ + for (int col = column - 1; col >= 0; col--) + { + Annotation annotation = annotations[col]; + if (annotation == null) + { + continue; + } + String displayed = annotation.displayCharacter; + if (displayed == null || displayed.length() != 1) + { + continue; + } + char symbol = displayed.charAt(0); + if (!Rna.isOpeningParenthesis(symbol)) + { + continue; + } + + /* + * found an opening bracket symbol + * count (closing-opening) symbols of this type that follow it, + * up to and excluding the target column; if the count is less + * than 1, the opening bracket is unmatched, so return its match + */ + String closer = String + .valueOf(Rna.getMatchingClosingParenthesis(symbol)); + String opener = String.valueOf(symbol); + int count = 0; + for (int j = col + 1; j < column; j++) + { + if (annotations[j] != null) + { + String s = annotations[j].displayCharacter; + if (closer.equals(s)) + { + count++; + } + else if (opener.equals(s)) + { + count--; + } + } + } + if (count < 1) + { + return closer; + } + } + return result; + } + protected static synchronized long nextId() { return counter++; } + + /** + * + * @return true for rows that have a range of values in their annotation set + */ + public boolean isQuantitative() + { + return graphMin < graphMax; + } }