2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.datamodel;
23 import java.util.Locale;
25 import jalview.analysis.Rna;
26 import jalview.analysis.SecStrConsensus.SimpleBP;
27 import jalview.analysis.WUSSParseException;
29 import java.util.ArrayList;
30 import java.util.Arrays;
31 import java.util.Collection;
32 import java.util.Collections;
33 import java.util.HashMap;
34 import java.util.Iterator;
35 import java.util.List;
37 import java.util.Map.Entry;
45 public class AlignmentAnnotation
47 private static final String ANNOTATION_ID_PREFIX = "ann";
50 * Identifers for different types of profile data
52 public static final int SEQUENCE_PROFILE = 0;
54 public static final int STRUCTURE_PROFILE = 1;
56 public static final int CDNA_PROFILE = 2;
58 private static long counter = 0;
61 * If true, this annotations is calculated every edit, eg consensus, quality
62 * or conservation graphs
64 public boolean autoCalculated = false;
67 * unique ID for this annotation, used to match up the same annotation row
68 * shown in multiple views and alignments
70 public String annotationId;
73 * the sequence this annotation is associated with (or null)
75 public SequenceI sequenceRef;
77 /** label shown in dropdown menus and in the annotation label area */
80 /** longer description text shown as a tooltip */
81 public String description;
83 /** Array of annotations placed in the current coordinate system */
84 public Annotation[] annotations;
86 public List<SimpleBP> bps = null;
89 * RNA secondary structure contact positions
91 public SequenceFeature[] _rnasecstr = null;
94 * position of annotation resulting in invalid WUSS parsing or -1. -2 means
95 * there was no RNA structure in this annotation
97 private long invalidrnastruc = -2;
100 * Updates the _rnasecstr field Determines the positions that base pair and
101 * the positions of helices based on secondary structure from a Stockholm file
103 * @param rnaAnnotation
105 private void _updateRnaSecStr(CharSequence rnaAnnotation)
109 _rnasecstr = Rna.getHelixMap(rnaAnnotation);
110 invalidrnastruc = -1;
111 } catch (WUSSParseException px)
113 // DEBUG System.out.println(px);
114 invalidrnastruc = px.getProblemPos();
116 if (invalidrnastruc > -1)
121 if (_rnasecstr != null && _rnasecstr.length > 0)
123 // show all the RNA secondary structure annotation symbols.
125 showAllColLabels = true;
126 scaleColLabel = true;
129 // System.out.println("featuregroup " + _rnasecstr[0].getFeatureGroup());
133 private void _markRnaHelices()
136 // Figure out number of helices
137 // Length of rnasecstr is the number of pairs of positions that base pair
138 // with each other in the secondary structure
139 for (int x = 0; x < _rnasecstr.length; x++)
143 * System.out.println(this.annotation._rnasecstr[x] + " Begin" +
144 * this.annotation._rnasecstr[x].getBegin());
146 // System.out.println(this.annotation._rnasecstr[x].getFeatureGroup());
150 val = Integer.valueOf(_rnasecstr[x].getFeatureGroup());
155 } catch (NumberFormatException q)
160 annotations[_rnasecstr[x].getBegin()].value = val;
161 annotations[_rnasecstr[x].getEnd()].value = val;
163 // annotations[_rnasecstr[x].getBegin()].displayCharacter = "" + val;
164 // annotations[_rnasecstr[x].getEnd()].displayCharacter = "" + val;
170 * Get the RNA Secondary Structure SequenceFeature Array if present
172 public SequenceFeature[] getRnaSecondaryStructure()
174 return this._rnasecstr;
178 * Check the RNA Secondary Structure is equivalent to one in given
179 * AlignmentAnnotation param
181 public boolean rnaSecondaryStructureEquivalent(AlignmentAnnotation that)
183 return rnaSecondaryStructureEquivalent(that, true);
186 public boolean rnaSecondaryStructureEquivalent(AlignmentAnnotation that, boolean compareType)
188 SequenceFeature[] thisSfArray = this.getRnaSecondaryStructure();
189 SequenceFeature[] thatSfArray = that.getRnaSecondaryStructure();
190 if (thisSfArray == null || thatSfArray == null)
192 return thisSfArray == null && thatSfArray == null;
194 if (thisSfArray.length != thatSfArray.length)
198 Arrays.sort(thisSfArray, new SFSortByEnd()); // probably already sorted
200 Arrays.sort(thatSfArray, new SFSortByEnd()); // probably already sorted
202 for (int i=0; i < thisSfArray.length; i++) {
203 SequenceFeature thisSf = thisSfArray[i];
204 SequenceFeature thatSf = thatSfArray[i];
206 if (thisSf.getType() == null || thatSf.getType() == null) {
207 if (thisSf.getType() == null && thatSf.getType() == null) {
213 if (! thisSf.getType().equals(thatSf.getType())) {
217 if (!(thisSf.getBegin() == thatSf.getBegin()
218 && thisSf.getEnd() == thatSf.getEnd()))
228 * map of positions in the associated annotation
230 private Map<Integer, Annotation> sequenceMapping;
233 * lower range for quantitative data
235 public float graphMin;
238 * Upper range for quantitative data
240 public float graphMax;
243 * Score associated with label and description.
245 public double score = Double.NaN;
248 * flag indicating if annotation has a score.
250 public boolean hasScore = false;
252 public GraphLine threshold;
254 // Graphical hints and tips
256 /** Can this row be edited by the user ? */
257 public boolean editable = false;
259 /** Indicates if annotation has a graphical symbol track */
260 public boolean hasIcons; //
262 /** Indicates if annotation has a text character label */
263 public boolean hasText;
265 /** is the row visible */
266 public boolean visible = true;
268 public int graphGroup = -1;
270 /** Displayed height of row in pixels */
271 public int height = 0;
273 public int graph = 0;
275 public int graphHeight = 40;
277 public boolean padGaps = false;
279 public static final int NO_GRAPH = 0;
281 public static final int BAR_GRAPH = 1;
283 public static final int LINE_GRAPH = 2;
285 public static final int CUSTOMRENDERER = 4;
287 public boolean belowAlignment = true;
289 public SequenceGroup groupRef = null;
292 * display every column label, even if there is a row of identical labels
294 public boolean showAllColLabels = false;
297 * scale the column label to fit within the alignment column.
299 public boolean scaleColLabel = false;
302 * centre the column labels relative to the alignment column
304 public boolean centreColLabels = false;
306 private boolean isrna;
308 public static int getGraphValueFromString(String string)
310 if (string.equalsIgnoreCase("BAR_GRAPH"))
314 else if (string.equalsIgnoreCase("LINE_GRAPH"))
325 * Creates a new AlignmentAnnotation object.
328 * short label shown under sequence labels
330 * text displayed on mouseover
332 * set of positional annotation elements
334 public AlignmentAnnotation(String label, String description,
335 Annotation[] annotations)
341 this.description = description;
342 this.annotations = annotations;
344 validateRangeAndDisplay();
348 * Checks if annotation labels represent secondary structures
351 void areLabelsSecondaryStructure()
353 boolean nonSSLabel = false;
355 StringBuffer rnastring = new StringBuffer();
358 for (int i = 0; i < annotations.length; i++)
360 // DEBUG System.out.println(i + ": " + annotations[i]);
361 if (annotations[i] == null)
365 if (annotations[i].secondaryStructure == 'H'
366 || annotations[i].secondaryStructure == 'E')
368 // DEBUG System.out.println( "/H|E/ '" +
369 // annotations[i].secondaryStructure + "'");
373 // Check for RNA secondary structure
375 // DEBUG System.out.println( "/else/ '" +
376 // annotations[i].secondaryStructure + "'");
377 // TODO: 2.8.2 should this ss symbol validation check be a function in
378 // RNA/ResidueProperties ?
379 if (annotations[i].secondaryStructure == '('
380 || annotations[i].secondaryStructure == '['
381 || annotations[i].secondaryStructure == '<'
382 || annotations[i].secondaryStructure == '{'
383 || annotations[i].secondaryStructure == 'A'
384 || annotations[i].secondaryStructure == 'B'
385 || annotations[i].secondaryStructure == 'C'
386 || annotations[i].secondaryStructure == 'D'
387 // || annotations[i].secondaryStructure == 'E' // ambiguous on
388 // its own -- already checked above
389 || annotations[i].secondaryStructure == 'F'
390 || annotations[i].secondaryStructure == 'G'
391 // || annotations[i].secondaryStructure == 'H' // ambiguous on
392 // its own -- already checked above
393 || annotations[i].secondaryStructure == 'I'
394 || annotations[i].secondaryStructure == 'J'
395 || annotations[i].secondaryStructure == 'K'
396 || annotations[i].secondaryStructure == 'L'
397 || annotations[i].secondaryStructure == 'M'
398 || annotations[i].secondaryStructure == 'N'
399 || annotations[i].secondaryStructure == 'O'
400 || annotations[i].secondaryStructure == 'P'
401 || annotations[i].secondaryStructure == 'Q'
402 || annotations[i].secondaryStructure == 'R'
403 || annotations[i].secondaryStructure == 'S'
404 || annotations[i].secondaryStructure == 'T'
405 || annotations[i].secondaryStructure == 'U'
406 || annotations[i].secondaryStructure == 'V'
407 || annotations[i].secondaryStructure == 'W'
408 || annotations[i].secondaryStructure == 'X'
409 || annotations[i].secondaryStructure == 'Y'
410 || annotations[i].secondaryStructure == 'Z')
417 // System.out.println("displaychar " + annotations[i].displayCharacter);
419 if (annotations[i].displayCharacter == null
420 || annotations[i].displayCharacter.length() == 0)
422 rnastring.append('.');
425 if (annotations[i].displayCharacter.length() == 1)
427 firstChar = annotations[i].displayCharacter.charAt(0);
428 // check to see if it looks like a sequence or is secondary structure
430 if (annotations[i].secondaryStructure != ' ' && !hasIcons &&
431 // Uncomment to only catch case where
432 // displayCharacter==secondary
434 // to correctly redisplay SS annotation imported from Stockholm,
435 // exported to JalviewXML and read back in again.
437 // annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure
438 firstChar != ' ' && firstChar != '$' && firstChar != 0xCE
439 && firstChar != '(' && firstChar != '[' && firstChar != '<'
440 && firstChar != '{' && firstChar != 'A' && firstChar != 'B'
441 && firstChar != 'C' && firstChar != 'D' && firstChar != 'E'
442 && firstChar != 'F' && firstChar != 'G' && firstChar != 'H'
443 && firstChar != 'I' && firstChar != 'J' && firstChar != 'K'
444 && firstChar != 'L' && firstChar != 'M' && firstChar != 'N'
445 && firstChar != 'O' && firstChar != 'P' && firstChar != 'Q'
446 && firstChar != 'R' && firstChar != 'S' && firstChar != 'T'
447 && firstChar != 'U' && firstChar != 'V' && firstChar != 'W'
448 && firstChar != 'X' && firstChar != 'Y' && firstChar != 'Z'
450 && firstChar < jalview.schemes.ResidueProperties.aaIndex.length)
452 if (jalview.schemes.ResidueProperties.aaIndex[firstChar] < 23) // TODO:
465 rnastring.append(annotations[i].displayCharacter.charAt(1));
468 if (annotations[i].displayCharacter.length() > 0)
477 for (int j = 0; j < annotations.length; j++)
479 if (annotations[j] != null
480 && annotations[j].secondaryStructure != ' ')
482 annotations[j].displayCharacter = String
483 .valueOf(annotations[j].secondaryStructure);
484 annotations[j].secondaryStructure = ' ';
493 _updateRnaSecStr(new AnnotCharSequence());
499 * flyweight access to positions in the alignment annotation row for RNA
505 private class AnnotCharSequence implements CharSequence
511 public AnnotCharSequence()
513 this(0, annotations.length);
516 AnnotCharSequence(int start, int end)
523 public CharSequence subSequence(int start, int end)
525 return new AnnotCharSequence(offset + start, offset + end);
535 public char charAt(int index)
537 return ((index + offset < 0) || (index + offset) >= max
538 || annotations[index + offset] == null
539 || (annotations[index + offset].secondaryStructure <= ' ')
541 : annotations[index + offset].displayCharacter == null
543 + offset].displayCharacter
546 + offset].secondaryStructure
548 + offset].displayCharacter
553 public String toString()
555 char[] string = new char[max - offset];
556 int mx = annotations.length;
558 for (int i = offset; i < mx; i++)
560 string[i] = (annotations[i] == null
561 || (annotations[i].secondaryStructure <= 32))
563 : (annotations[i].displayCharacter == null
564 || annotations[i].displayCharacter
566 ? annotations[i].secondaryStructure
567 : annotations[i].displayCharacter
570 return new String(string);
574 private long _lastrnaannot = -1;
576 public String getRNAStruc()
580 String rnastruc = new AnnotCharSequence().toString();
581 if (_lastrnaannot != rnastruc.hashCode())
583 // ensure rna structure contacts are up to date
584 _lastrnaannot = rnastruc.hashCode();
585 _updateRnaSecStr(rnastruc);
593 * Creates a new AlignmentAnnotation object.
608 public AlignmentAnnotation(String label, String description,
609 Annotation[] annotations, float min, float max, int graphType)
612 // graphs are not editable
613 editable = graphType == 0;
616 this.description = description;
617 this.annotations = annotations;
621 validateRangeAndDisplay();
625 * checks graphMin and graphMax, secondary structure symbols, sets graphType
626 * appropriately, sets null labels to the empty string if appropriate.
628 public void validateRangeAndDisplay()
631 if (annotations == null)
633 visible = false; // try to prevent renderer from displaying.
634 invalidrnastruc = -1;
635 return; // this is a non-annotation row annotation - ie a sequence score.
638 int graphType = graph;
639 float min = graphMin;
640 float max = graphMax;
641 boolean drawValues = true;
646 for (int i = 0; i < annotations.length; i++)
648 if (annotations[i] == null)
653 if (drawValues && annotations[i].displayCharacter != null
654 && annotations[i].displayCharacter.length() > 1)
659 if (annotations[i].value > max)
661 max = annotations[i].value;
664 if (annotations[i].value < min)
666 min = annotations[i].value;
668 if (_linecolour == null && annotations[i].colour != null)
670 _linecolour = annotations[i].colour;
673 // ensure zero is origin for min/max ranges on only one side of zero
690 areLabelsSecondaryStructure();
692 if (!drawValues && graphType != NO_GRAPH)
694 for (int i = 0; i < annotations.length; i++)
696 if (annotations[i] != null)
698 annotations[i].displayCharacter = "";
705 * Copy constructor creates a new independent annotation row with the same
706 * associated sequenceRef
710 public AlignmentAnnotation(AlignmentAnnotation annotation)
713 this.label = new String(annotation.label);
714 if (annotation.description != null)
716 this.description = new String(annotation.description);
718 this.graphMin = annotation.graphMin;
719 this.graphMax = annotation.graphMax;
720 this.graph = annotation.graph;
721 this.graphHeight = annotation.graphHeight;
722 this.graphGroup = annotation.graphGroup;
723 this.groupRef = annotation.groupRef;
724 this.editable = annotation.editable;
725 this.autoCalculated = annotation.autoCalculated;
726 this.hasIcons = annotation.hasIcons;
727 this.hasText = annotation.hasText;
728 this.height = annotation.height;
729 this.label = annotation.label;
730 this.padGaps = annotation.padGaps;
731 this.visible = annotation.visible;
732 this.centreColLabels = annotation.centreColLabels;
733 this.scaleColLabel = annotation.scaleColLabel;
734 this.showAllColLabels = annotation.showAllColLabels;
735 this.calcId = annotation.calcId;
736 if (annotation.properties != null)
738 properties = new HashMap<>();
739 for (Map.Entry<String, String> val : annotation.properties.entrySet())
741 properties.put(val.getKey(), val.getValue());
744 if (this.hasScore = annotation.hasScore)
746 this.score = annotation.score;
748 if (annotation.threshold != null)
750 threshold = new GraphLine(annotation.threshold);
752 Annotation[] ann = annotation.annotations;
753 if (annotation.annotations != null)
755 this.annotations = new Annotation[ann.length];
756 for (int i = 0; i < ann.length; i++)
760 annotations[i] = new Annotation(ann[i]);
761 if (_linecolour != null)
763 _linecolour = annotations[i].colour;
768 if (annotation.sequenceRef != null)
770 this.sequenceRef = annotation.sequenceRef;
771 if (annotation.sequenceMapping != null)
774 sequenceMapping = new HashMap<>();
775 Iterator<Integer> pos = annotation.sequenceMapping.keySet()
777 while (pos.hasNext())
779 // could optimise this!
781 Annotation a = annotation.sequenceMapping.get(p);
788 for (int i = 0; i < ann.length; i++)
792 sequenceMapping.put(p, annotations[i]);
800 this.sequenceMapping = null;
803 // TODO: check if we need to do this: JAL-952
804 // if (this.isrna=annotation.isrna)
806 // _rnasecstr=new SequenceFeature[annotation._rnasecstr];
808 validateRangeAndDisplay(); // construct hashcodes, etc.
812 * clip the annotation to the columns given by startRes and endRes (inclusive)
813 * and prune any existing sequenceMapping to just those columns.
818 public void restrict(int startRes, int endRes)
820 if (annotations == null)
829 if (startRes >= annotations.length)
831 startRes = annotations.length - 1;
833 if (endRes >= annotations.length)
835 endRes = annotations.length - 1;
837 if (annotations == null)
841 Annotation[] temp = new Annotation[endRes - startRes + 1];
842 if (startRes < annotations.length)
844 System.arraycopy(annotations, startRes, temp, 0,
845 endRes - startRes + 1);
847 if (sequenceRef != null)
849 // Clip the mapping, if it exists.
850 int spos = sequenceRef.findPosition(startRes);
851 int epos = sequenceRef.findPosition(endRes);
852 if (sequenceMapping != null)
854 Map<Integer, Annotation> newmapping = new HashMap<>();
855 Iterator<Integer> e = sequenceMapping.keySet().iterator();
858 Integer pos = e.next();
859 if (pos.intValue() >= spos && pos.intValue() <= epos)
861 newmapping.put(pos, sequenceMapping.get(pos));
864 sequenceMapping.clear();
865 sequenceMapping = newmapping;
872 * set the annotation row to be at least length Annotations
875 * minimum number of columns required in the annotation row
876 * @return false if the annotation row is greater than length
878 public boolean padAnnotation(int length)
880 if (annotations == null)
882 return true; // annotation row is correct - null == not visible and
885 if (annotations.length < length)
887 Annotation[] na = new Annotation[length];
888 System.arraycopy(annotations, 0, na, 0, annotations.length);
892 return annotations.length > length;
899 * @return DOCUMENT ME!
902 public String toString()
904 if (annotations == null)
908 StringBuilder buffer = new StringBuilder(256);
910 for (int i = 0; i < annotations.length; i++)
912 if (annotations[i] != null)
916 buffer.append(annotations[i].value);
920 buffer.append(annotations[i].secondaryStructure);
924 buffer.append(annotations[i].displayCharacter);
930 // TODO: remove disgusting hack for 'special' treatment of consensus line.
931 if (label.indexOf("Consensus") == 0)
935 for (int i = 0; i < annotations.length; i++)
937 if (annotations[i] != null)
939 buffer.append(annotations[i].description);
946 return buffer.toString();
949 public void setThreshold(GraphLine line)
954 public GraphLine getThreshold()
960 * Attach the annotation to seqRef, starting from startRes position. If
961 * alreadyMapped is true then the indices of the annotation[] array are
962 * sequence positions rather than alignment column positions.
966 * @param alreadyMapped
968 public void createSequenceMapping(SequenceI seqRef, int startRes,
969 boolean alreadyMapped)
976 sequenceRef = seqRef;
977 if (annotations == null)
981 sequenceMapping = new HashMap<>();
985 for (int i = 0; i < annotations.length; i++)
987 if (annotations[i] != null)
991 seqPos = seqRef.findPosition(i);
995 seqPos = i + startRes;
998 sequenceMapping.put(Integer.valueOf(seqPos), annotations[i]);
1005 * When positional annotation and a sequence reference is present, clears and
1006 * resizes the annotations array to the current alignment width, and adds
1007 * annotation according to aligned positions of the sequenceRef given by
1010 public void adjustForAlignment()
1012 if (sequenceRef == null)
1017 if (annotations == null)
1022 int a = 0, aSize = sequenceRef.getLength();
1031 Annotation[] temp = new Annotation[aSize];
1033 if (sequenceMapping != null)
1035 for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++)
1037 index = Integer.valueOf(a);
1038 Annotation annot = sequenceMapping.get(index);
1041 position = sequenceRef.findIndex(a) - 1;
1043 temp[position] = annot;
1051 * remove any null entries in annotation row and return the number of non-null
1052 * annotation elements.
1056 public int compactAnnotationArray()
1058 int i = 0, iSize = annotations.length;
1061 if (annotations[i] == null)
1065 System.arraycopy(annotations, i + 1, annotations, i,
1075 Annotation[] ann = annotations;
1076 annotations = new Annotation[i];
1077 System.arraycopy(ann, 0, annotations, 0, i);
1083 * Associate this annotation with the aligned residues of a particular
1084 * sequence. sequenceMapping will be updated in the following way: null
1085 * sequenceI - existing mapping will be discarded but annotations left in
1086 * mapped positions. valid sequenceI not equal to current sequenceRef: mapping
1087 * is discarded and rebuilt assuming 1:1 correspondence TODO: overload with
1088 * parameter to specify correspondence between current and new sequenceRef
1092 public void setSequenceRef(SequenceI sequenceI)
1094 if (sequenceI != null)
1096 if (sequenceRef != null)
1098 boolean rIsDs = sequenceRef.getDatasetSequence() == null,
1099 tIsDs = sequenceI.getDatasetSequence() == null;
1100 if (sequenceRef != sequenceI
1102 && sequenceRef != sequenceI.getDatasetSequence())
1104 && sequenceRef.getDatasetSequence() != sequenceI)
1105 && (!rIsDs && !tIsDs
1106 && sequenceRef.getDatasetSequence() != sequenceI
1107 .getDatasetSequence())
1108 && !sequenceRef.equals(sequenceI))
1110 // if sequenceRef isn't intersecting with sequenceI
1111 // throw away old mapping and reconstruct.
1113 if (sequenceMapping != null)
1115 sequenceMapping = null;
1116 // compactAnnotationArray();
1118 createSequenceMapping(sequenceI, 1, true);
1119 adjustForAlignment();
1123 // Mapping carried over
1124 sequenceRef = sequenceI;
1129 // No mapping exists
1130 createSequenceMapping(sequenceI, 1, true);
1131 adjustForAlignment();
1136 // throw away the mapping without compacting.
1137 sequenceMapping = null;
1145 public double getScore()
1154 public void setScore(double score)
1162 * @return true if annotation has an associated score
1164 public boolean hasScore()
1166 return hasScore || !Double.isNaN(score);
1170 * Score only annotation
1173 * @param description
1176 public AlignmentAnnotation(String label, String description, double score)
1178 this(label, description, null);
1183 * copy constructor with edit based on the hidden columns marked in colSel
1185 * @param alignmentAnnotation
1188 public AlignmentAnnotation(AlignmentAnnotation alignmentAnnotation,
1189 HiddenColumns hidden)
1191 this(alignmentAnnotation);
1192 if (annotations == null)
1196 makeVisibleAnnotation(hidden);
1199 public void setPadGaps(boolean padgaps, char gapchar)
1201 this.padGaps = padgaps;
1205 for (int i = 0; i < annotations.length; i++)
1207 if (annotations[i] == null)
1209 annotations[i] = new Annotation(String.valueOf(gapchar), null,
1212 else if (annotations[i].displayCharacter == null
1213 || annotations[i].displayCharacter.equals(" "))
1215 annotations[i].displayCharacter = String.valueOf(gapchar);
1222 * format description string for display
1225 * @return Get the annotation description string optionally prefixed by
1226 * associated sequence name (if any)
1228 public String getDescription(boolean seqname)
1230 if (seqname && this.sequenceRef != null)
1232 int i = description.toLowerCase(Locale.ROOT).indexOf("<html>");
1235 // move the html tag to before the sequence reference.
1236 return "<html>" + sequenceRef.getName() + " : "
1237 + description.substring(i + 6);
1239 return sequenceRef.getName() + " : " + description;
1244 public boolean isValidStruc()
1246 return invalidrnastruc == -1;
1249 public long getInvalidStrucPos()
1251 return invalidrnastruc;
1255 * machine readable ID string indicating what generated this annotation
1257 protected String calcId = "";
1260 * properties associated with the calcId
1262 protected Map<String, String> properties = new HashMap<>();
1265 * base colour for line graphs. If null, will be set automatically by
1266 * searching the alignment annotation
1268 public java.awt.Color _linecolour;
1270 public String getCalcId()
1275 public void setCalcId(String calcId)
1277 this.calcId = calcId;
1280 public boolean isRNA()
1286 * transfer annotation to the given sequence using the given mapping from the
1287 * current positions or an existing sequence mapping
1291 * map involving sq as To or From
1293 public void liftOver(SequenceI sq, Mapping sp2sq)
1295 if (sp2sq.getMappedWidth() != sp2sq.getWidth())
1297 // TODO: employ getWord/MappedWord to transfer annotation between cDNA and
1298 // Protein reference frames
1300 "liftOver currently not implemented for transfer of annotation between different types of seqeunce");
1302 boolean mapIsTo = (sp2sq != null)
1303 ? (sp2sq.getTo() == sq
1304 || sp2sq.getTo() == sq.getDatasetSequence())
1307 // TODO build a better annotation element map and get rid of annotations[]
1308 Map<Integer, Annotation> mapForsq = new HashMap<>();
1309 if (sequenceMapping != null)
1313 for (Entry<Integer, Annotation> ie : sequenceMapping.entrySet())
1315 Integer mpos = Integer
1316 .valueOf(mapIsTo ? sp2sq.getMappedPosition(ie.getKey())
1317 : sp2sq.getPosition(ie.getKey()));
1318 if (mpos >= sq.getStart() && mpos <= sq.getEnd())
1320 mapForsq.put(mpos, ie.getValue());
1323 sequenceMapping = mapForsq;
1325 adjustForAlignment();
1335 * like liftOver but more general.
1337 * Takes an array of int pairs that will be used to update the internal
1338 * sequenceMapping and so shuffle the annotated positions
1341 * - new sequence reference for the annotation row - if null,
1342 * sequenceRef is left unchanged
1344 * array of ints containing corresponding positions
1346 * - column for current coordinate system (-1 for index+1)
1348 * - column for destination coordinate system (-1 for index+1)
1350 * - offset added to index when referencing either coordinate system
1351 * @note no checks are made as to whether from and/or to are sensible
1352 * @note caller should add the remapped annotation to newref if they have not
1355 public void remap(SequenceI newref, HashMap<Integer, int[]> mapping,
1356 int from, int to, int idxoffset)
1358 if (mapping != null)
1360 Map<Integer, Annotation> old = sequenceMapping;
1361 Map<Integer, Annotation> remap = new HashMap<>();
1363 for (int mp[] : mapping.values())
1369 Annotation ann = null;
1372 ann = sequenceMapping.get(Integer.valueOf(idxoffset + index));
1376 if (mp != null && mp.length > from)
1378 ann = sequenceMapping.get(Integer.valueOf(mp[from]));
1385 remap.put(Integer.valueOf(idxoffset + index), ann);
1389 if (to > -1 && to < mp.length)
1391 remap.put(Integer.valueOf(mp[to]), ann);
1396 sequenceMapping = remap;
1400 sequenceRef = newref;
1402 adjustForAlignment();
1406 public String getProperty(String property)
1408 if (properties == null)
1412 return properties.get(property);
1415 public void setProperty(String property, String value)
1417 if (properties == null)
1419 properties = new HashMap<>();
1421 properties.put(property, value);
1424 public boolean hasProperties()
1426 return properties != null && properties.size() > 0;
1429 public Collection<String> getProperties()
1431 if (properties == null)
1433 return Collections.emptyList();
1435 return properties.keySet();
1439 * Returns the Annotation for the given sequence position (base 1) if any,
1445 public Annotation getAnnotationForPosition(int position)
1447 return sequenceMapping == null ? null : sequenceMapping.get(position);
1452 * Set the id to "ann" followed by a counter that increments so as to be
1453 * unique for the lifetime of the JVM
1455 protected final void setAnnotationId()
1457 this.annotationId = ANNOTATION_ID_PREFIX + Long.toString(nextId());
1461 * Returns the match for the last unmatched opening RNA helix pair symbol
1462 * preceding the given column, or '(' if nothing found to match.
1467 public String getDefaultRnaHelixSymbol(int column)
1469 String result = "(";
1470 if (annotations == null)
1476 * for each preceding column, if it contains an open bracket,
1477 * count whether it is still unmatched at column, if so return its pair
1478 * (likely faster than the fancy alternative using stacks)
1480 for (int col = column - 1; col >= 0; col--)
1482 Annotation annotation = annotations[col];
1483 if (annotation == null)
1487 String displayed = annotation.displayCharacter;
1488 if (displayed == null || displayed.length() != 1)
1492 char symbol = displayed.charAt(0);
1493 if (!Rna.isOpeningParenthesis(symbol))
1499 * found an opening bracket symbol
1500 * count (closing-opening) symbols of this type that follow it,
1501 * up to and excluding the target column; if the count is less
1502 * than 1, the opening bracket is unmatched, so return its match
1504 String closer = String
1505 .valueOf(Rna.getMatchingClosingParenthesis(symbol));
1506 String opener = String.valueOf(symbol);
1508 for (int j = col + 1; j < column; j++)
1510 if (annotations[j] != null)
1512 String s = annotations[j].displayCharacter;
1513 if (closer.equals(s))
1517 else if (opener.equals(s))
1531 protected static synchronized long nextId()
1538 * @return true for rows that have a range of values in their annotation set
1540 public boolean isQuantitative()
1542 return graphMin < graphMax;
1546 * delete any columns in alignmentAnnotation that are hidden (including
1547 * sequence associated annotation).
1549 * @param hiddenColumns
1550 * the set of hidden columns
1552 public void makeVisibleAnnotation(HiddenColumns hiddenColumns)
1554 if (annotations != null)
1556 makeVisibleAnnotation(0, annotations.length, hiddenColumns);
1561 * delete any columns in alignmentAnnotation that are hidden (including
1562 * sequence associated annotation).
1565 * remove any annotation to the right of this column
1567 * remove any annotation to the left of this column
1568 * @param hiddenColumns
1569 * the set of hidden columns
1571 public void makeVisibleAnnotation(int start, int end,
1572 HiddenColumns hiddenColumns)
1574 if (annotations != null)
1576 if (hiddenColumns.hasHiddenColumns())
1578 removeHiddenAnnotation(start, end, hiddenColumns);
1582 restrict(start, end);
1588 * The actual implementation of deleting hidden annotation columns
1591 * remove any annotation to the right of this column
1593 * remove any annotation to the left of this column
1594 * @param hiddenColumns
1595 * the set of hidden columns
1597 private void removeHiddenAnnotation(int start, int end,
1598 HiddenColumns hiddenColumns)
1600 // mangle the alignmentAnnotation annotation array
1601 ArrayList<Annotation[]> annels = new ArrayList<>();
1602 Annotation[] els = null;
1606 Iterator<int[]> blocks = hiddenColumns.getVisContigsIterator(start,
1610 int annotationLength;
1611 while (blocks.hasNext())
1613 int[] block = blocks.next();
1614 annotationLength = block[1] - block[0] + 1;
1616 if (blocks.hasNext())
1618 // copy just the visible segment of the annotation row
1619 copylength = annotationLength;
1623 if (annotationLength + block[0] <= annotations.length)
1625 // copy just the visible segment of the annotation row
1626 copylength = annotationLength;
1630 // copy to the end of the annotation row
1631 copylength = annotations.length - block[0];
1635 els = new Annotation[annotationLength];
1637 System.arraycopy(annotations, block[0], els, 0, copylength);
1638 w += annotationLength;
1643 annotations = new Annotation[w];
1646 for (Annotation[] chnk : annels)
1648 System.arraycopy(chnk, 0, annotations, w, chnk.length);
1654 public static Iterable<AlignmentAnnotation> findAnnotations(
1655 Iterable<AlignmentAnnotation> list, SequenceI seq, String calcId,
1659 ArrayList<AlignmentAnnotation> aa = new ArrayList<>();
1660 for (AlignmentAnnotation ann : list)
1662 if ((calcId == null || (ann.getCalcId() != null
1663 && ann.getCalcId().equals(calcId)))
1664 && (seq == null || (ann.sequenceRef != null
1665 && ann.sequenceRef == seq))
1667 || (ann.label != null && ann.label.equals(label))))
1676 * Answer true if any annotation matches the calcId passed in (if not null).
1679 * annotation to search
1683 public static boolean hasAnnotation(List<AlignmentAnnotation> list,
1687 if (calcId != null && !"".equals(calcId))
1689 for (AlignmentAnnotation a : list)
1691 if (a.getCalcId() == calcId)
1700 public static Iterable<AlignmentAnnotation> findAnnotation(
1701 List<AlignmentAnnotation> list, String calcId)
1704 List<AlignmentAnnotation> aa = new ArrayList<>();
1709 for (AlignmentAnnotation a : list)
1712 if (a.getCalcId() == calcId || (a.getCalcId() != null
1713 && calcId != null && a.getCalcId().equals(calcId)))