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 jalview.analysis.Rna;
24 import jalview.analysis.SecStrConsensus.SimpleBP;
25 import jalview.analysis.WUSSParseException;
27 import java.util.ArrayList;
28 import java.util.Arrays;
29 import java.util.Collection;
30 import java.util.Collections;
31 import java.util.HashMap;
32 import java.util.Iterator;
33 import java.util.List;
35 import java.util.Map.Entry;
43 public class AlignmentAnnotation
45 private static final String ANNOTATION_ID_PREFIX = "ann";
48 * Identifers for different types of profile data
50 public static final int SEQUENCE_PROFILE = 0;
52 public static final int STRUCTURE_PROFILE = 1;
54 public static final int CDNA_PROFILE = 2;
56 private static long counter = 0;
59 * If true, this annotations is calculated every edit, eg consensus, quality
60 * or conservation graphs
62 public boolean autoCalculated = false;
65 * unique ID for this annotation, used to match up the same annotation row
66 * shown in multiple views and alignments
68 public String annotationId;
71 * the sequence this annotation is associated with (or null)
73 public SequenceI sequenceRef;
75 /** label shown in dropdown menus and in the annotation label area */
78 /** longer description text shown as a tooltip */
79 public String description;
81 /** Array of annotations placed in the current coordinate system */
82 public Annotation[] annotations;
84 public List<SimpleBP> bps = null;
87 * RNA secondary structure contact positions
89 public SequenceFeature[] _rnasecstr = null;
92 * position of annotation resulting in invalid WUSS parsing or -1. -2 means
93 * there was no RNA structure in this annotation
95 private long invalidrnastruc = -2;
97 private double bitScore;
99 private double eValue;
102 * Updates the _rnasecstr field Determines the positions that base pair and
103 * the positions of helices based on secondary structure from a Stockholm file
105 * @param rnaAnnotation
107 private void _updateRnaSecStr(CharSequence rnaAnnotation)
111 _rnasecstr = Rna.getHelixMap(rnaAnnotation);
112 invalidrnastruc = -1;
113 } catch (WUSSParseException px)
115 // DEBUG System.out.println(px);
116 invalidrnastruc = px.getProblemPos();
118 if (invalidrnastruc > -1)
123 if (_rnasecstr != null && _rnasecstr.length > 0)
125 // show all the RNA secondary structure annotation symbols.
127 showAllColLabels = true;
128 scaleColLabel = true;
131 // System.out.println("featuregroup " + _rnasecstr[0].getFeatureGroup());
135 private void _markRnaHelices()
138 // Figure out number of helices
139 // Length of rnasecstr is the number of pairs of positions that base pair
140 // with each other in the secondary structure
141 for (int x = 0; x < _rnasecstr.length; x++)
145 * System.out.println(this.annotation._rnasecstr[x] + " Begin" +
146 * this.annotation._rnasecstr[x].getBegin());
148 // System.out.println(this.annotation._rnasecstr[x].getFeatureGroup());
152 val = Integer.valueOf(_rnasecstr[x].getFeatureGroup());
157 } catch (NumberFormatException q)
162 annotations[_rnasecstr[x].getBegin()].value = val;
163 annotations[_rnasecstr[x].getEnd()].value = val;
165 // annotations[_rnasecstr[x].getBegin()].displayCharacter = "" + val;
166 // annotations[_rnasecstr[x].getEnd()].displayCharacter = "" + val;
172 * Get the RNA Secondary Structure SequenceFeature Array if present
174 public SequenceFeature[] getRnaSecondaryStructure()
176 return this._rnasecstr;
180 * Check the RNA Secondary Structure is equivalent to one in given
181 * AlignmentAnnotation param
183 public boolean rnaSecondaryStructureEquivalent(AlignmentAnnotation that)
185 return rnaSecondaryStructureEquivalent(that, true);
188 public boolean rnaSecondaryStructureEquivalent(AlignmentAnnotation that, boolean compareType)
190 SequenceFeature[] thisSfArray = this.getRnaSecondaryStructure();
191 SequenceFeature[] thatSfArray = that.getRnaSecondaryStructure();
192 if (thisSfArray == null || thatSfArray == null)
194 return thisSfArray == null && thatSfArray == null;
196 if (thisSfArray.length != thatSfArray.length)
200 Arrays.sort(thisSfArray, new SFSortByEnd()); // probably already sorted
202 Arrays.sort(thatSfArray, new SFSortByEnd()); // probably already sorted
204 for (int i=0; i < thisSfArray.length; i++) {
205 SequenceFeature thisSf = thisSfArray[i];
206 SequenceFeature thatSf = thatSfArray[i];
208 if (thisSf.getType() == null || thatSf.getType() == null) {
209 if (thisSf.getType() == null && thatSf.getType() == null) {
215 if (! thisSf.getType().equals(thatSf.getType())) {
219 if (!(thisSf.getBegin() == thatSf.getBegin()
220 && thisSf.getEnd() == thatSf.getEnd()))
230 * map of positions in the associated annotation
232 private Map<Integer, Annotation> sequenceMapping;
235 * lower range for quantitative data
237 public float graphMin;
240 * Upper range for quantitative data
242 public float graphMax;
245 * Score associated with label and description.
247 public double score = Double.NaN;
250 * flag indicating if annotation has a score.
252 public boolean hasScore = false;
254 public GraphLine threshold;
256 // Graphical hints and tips
258 /** Can this row be edited by the user ? */
259 public boolean editable = false;
261 /** Indicates if annotation has a graphical symbol track */
262 public boolean hasIcons; //
264 /** Indicates if annotation has a text character label */
265 public boolean hasText;
267 /** is the row visible */
268 public boolean visible = true;
270 public int graphGroup = -1;
272 /** Displayed height of row in pixels */
273 public int height = 0;
275 public int graph = 0;
277 public int graphHeight = 40;
279 public boolean padGaps = false;
281 public static final int NO_GRAPH = 0;
283 public static final int BAR_GRAPH = 1;
285 public static final int LINE_GRAPH = 2;
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
967 * - annotation are at aligned columns
969 public void createSequenceMapping(SequenceI seqRef, int startRes,
970 boolean alreadyMapped)
977 sequenceRef = seqRef;
978 if (annotations == null)
982 sequenceMapping = new HashMap<>();
986 for (int i = 0; i < annotations.length; i++)
988 if (annotations[i] != null)
992 seqPos = seqRef.findPosition(i);
996 seqPos = i + startRes;
999 sequenceMapping.put(Integer.valueOf(seqPos), annotations[i]);
1006 * When positional annotation and a sequence reference is present, clears and
1007 * resizes the annotations array to the current alignment width, and adds
1008 * annotation according to aligned positions of the sequenceRef given by
1011 public void adjustForAlignment()
1013 if (sequenceRef == null)
1018 if (annotations == null)
1023 int a = 0, aSize = sequenceRef.getLength();
1032 Annotation[] temp = new Annotation[aSize];
1034 if (sequenceMapping != null)
1036 for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++)
1038 index = Integer.valueOf(a);
1039 Annotation annot = sequenceMapping.get(index);
1042 position = sequenceRef.findIndex(a) - 1;
1044 temp[position] = annot;
1052 * remove any null entries in annotation row and return the number of non-null
1053 * annotation elements.
1057 public int compactAnnotationArray()
1059 int i = 0, iSize = annotations.length;
1062 if (annotations[i] == null)
1066 System.arraycopy(annotations, i + 1, annotations, i,
1076 Annotation[] ann = annotations;
1077 annotations = new Annotation[i];
1078 System.arraycopy(ann, 0, annotations, 0, i);
1084 * Associate this annotation with the aligned residues of a particular
1085 * sequence. sequenceMapping will be updated in the following way: null
1086 * sequenceI - existing mapping will be discarded but annotations left in
1087 * mapped positions. valid sequenceI not equal to current sequenceRef: mapping
1088 * is discarded and rebuilt assuming 1:1 correspondence TODO: overload with
1089 * parameter to specify correspondence between current and new sequenceRef
1093 public void setSequenceRef(SequenceI sequenceI)
1095 if (sequenceI != null)
1097 if (sequenceRef != null)
1099 boolean rIsDs = sequenceRef.getDatasetSequence() == null,
1100 tIsDs = sequenceI.getDatasetSequence() == null;
1101 if (sequenceRef != sequenceI
1103 && sequenceRef != sequenceI.getDatasetSequence())
1105 && sequenceRef.getDatasetSequence() != sequenceI)
1106 && (!rIsDs && !tIsDs
1107 && sequenceRef.getDatasetSequence() != sequenceI
1108 .getDatasetSequence())
1109 && !sequenceRef.equals(sequenceI))
1111 // if sequenceRef isn't intersecting with sequenceI
1112 // throw away old mapping and reconstruct.
1114 if (sequenceMapping != null)
1116 sequenceMapping = null;
1117 // compactAnnotationArray();
1119 createSequenceMapping(sequenceI, 1, true);
1120 adjustForAlignment();
1124 // Mapping carried over
1125 sequenceRef = sequenceI;
1130 // No mapping exists
1131 createSequenceMapping(sequenceI, 1, true);
1132 adjustForAlignment();
1137 // throw away the mapping without compacting.
1138 sequenceMapping = null;
1146 public double getScore()
1155 public void setScore(double score)
1163 * @return true if annotation has an associated score
1165 public boolean hasScore()
1167 return hasScore || !Double.isNaN(score);
1171 * Score only annotation
1174 * @param description
1177 public AlignmentAnnotation(String label, String description, double score)
1179 this(label, description, null);
1184 * copy constructor with edit based on the hidden columns marked in colSel
1186 * @param alignmentAnnotation
1189 public AlignmentAnnotation(AlignmentAnnotation alignmentAnnotation,
1190 HiddenColumns hidden)
1192 this(alignmentAnnotation);
1193 if (annotations == null)
1197 makeVisibleAnnotation(hidden);
1201 public void setPadGaps(boolean padgaps, char gapchar)
1203 this.padGaps = padgaps;
1207 for (int i = 0; i < annotations.length; i++)
1209 if (annotations[i] == null)
1211 annotations[i] = new Annotation(String.valueOf(gapchar), null,
1214 else if (annotations[i].displayCharacter == null
1215 || annotations[i].displayCharacter.equals(" "))
1217 annotations[i].displayCharacter = String.valueOf(gapchar);
1224 * format description string for display
1227 * @return Get the annotation description string optionally prefixed by
1228 * associated sequence name (if any)
1230 public String getDescription(boolean seqname)
1232 if (seqname && this.sequenceRef != null)
1234 int i = description.toLowerCase().indexOf("<html>");
1237 // move the html tag to before the sequence reference.
1238 return "<html>" + sequenceRef.getName() + " : "
1239 + description.substring(i + 6);
1241 return sequenceRef.getName() + " : " + description;
1246 public boolean isValidStruc()
1248 return invalidrnastruc == -1;
1251 public long getInvalidStrucPos()
1253 return invalidrnastruc;
1257 * machine readable ID string indicating what generated this annotation
1259 protected String calcId = "";
1262 * properties associated with the calcId
1264 protected Map<String, String> properties = new HashMap<>();
1267 * base colour for line graphs. If null, will be set automatically by
1268 * searching the alignment annotation
1270 public java.awt.Color _linecolour;
1272 public String getCalcId()
1277 public void setCalcId(String calcId)
1279 this.calcId = calcId;
1282 public boolean isRNA()
1288 * transfer annotation to the given sequence using the given mapping from the
1289 * current positions or an existing sequence mapping
1293 * map involving sq as To or From
1295 public void liftOver(SequenceI sq, Mapping sp2sq)
1297 if (sp2sq.getMappedWidth() != sp2sq.getWidth())
1299 // TODO: employ getWord/MappedWord to transfer annotation between cDNA and
1300 // Protein reference frames
1302 "liftOver currently not implemented for transfer of annotation between different types of seqeunce");
1304 boolean mapIsTo = (sp2sq != null)
1305 ? (sp2sq.getTo() == sq
1306 || sp2sq.getTo() == sq.getDatasetSequence())
1309 // TODO build a better annotation element map and get rid of annotations[]
1310 Map<Integer, Annotation> mapForsq = new HashMap<>();
1311 if (sequenceMapping != null)
1315 for (Entry<Integer, Annotation> ie : sequenceMapping.entrySet())
1317 Integer mpos = Integer
1318 .valueOf(mapIsTo ? sp2sq.getMappedPosition(ie.getKey())
1319 : sp2sq.getPosition(ie.getKey()));
1320 if (mpos >= sq.getStart() && mpos <= sq.getEnd())
1322 mapForsq.put(mpos, ie.getValue());
1325 sequenceMapping = mapForsq;
1327 adjustForAlignment();
1337 * like liftOver but more general.
1339 * Takes an array of int pairs that will be used to update the internal
1340 * sequenceMapping and so shuffle the annotated positions
1343 * - new sequence reference for the annotation row - if null,
1344 * sequenceRef is left unchanged
1346 * array of ints containing corresponding positions
1348 * - column for current coordinate system (-1 for index+1)
1350 * - column for destination coordinate system (-1 for index+1)
1352 * - offset added to index when referencing either coordinate system
1353 * @note no checks are made as to whether from and/or to are sensible
1354 * @note caller should add the remapped annotation to newref if they have not
1357 public void remap(SequenceI newref, HashMap<Integer, int[]> mapping,
1358 int from, int to, int idxoffset)
1360 if (mapping != null)
1362 Map<Integer, Annotation> old = sequenceMapping;
1363 Map<Integer, Annotation> remap = new HashMap<>();
1365 for (int mp[] : mapping.values())
1371 Annotation ann = null;
1374 ann = sequenceMapping.get(Integer.valueOf(idxoffset + index));
1378 if (mp != null && mp.length > from)
1380 ann = sequenceMapping.get(Integer.valueOf(mp[from]));
1387 remap.put(Integer.valueOf(idxoffset + index), ann);
1391 if (to > -1 && to < mp.length)
1393 remap.put(Integer.valueOf(mp[to]), ann);
1398 sequenceMapping = remap;
1402 sequenceRef = newref;
1404 adjustForAlignment();
1408 public String getProperty(String property)
1410 if (properties == null)
1414 return properties.get(property);
1417 public void setProperty(String property, String value)
1419 if (properties == null)
1421 properties = new HashMap<>();
1423 properties.put(property, value);
1426 public boolean hasProperties()
1428 return properties != null && properties.size() > 0;
1431 public Collection<String> getProperties()
1433 if (properties == null)
1435 return Collections.emptyList();
1437 return properties.keySet();
1441 * Returns the Annotation for the given sequence position (base 1) if any,
1447 public Annotation getAnnotationForPosition(int position)
1449 return sequenceMapping == null ? null : sequenceMapping.get(position);
1454 * Set the id to "ann" followed by a counter that increments so as to be
1455 * unique for the lifetime of the JVM
1457 protected final void setAnnotationId()
1459 this.annotationId = ANNOTATION_ID_PREFIX + Long.toString(nextId());
1463 * Returns the match for the last unmatched opening RNA helix pair symbol
1464 * preceding the given column, or '(' if nothing found to match.
1469 public String getDefaultRnaHelixSymbol(int column)
1471 String result = "(";
1472 if (annotations == null)
1478 * for each preceding column, if it contains an open bracket,
1479 * count whether it is still unmatched at column, if so return its pair
1480 * (likely faster than the fancy alternative using stacks)
1482 for (int col = column - 1; col >= 0; col--)
1484 Annotation annotation = annotations[col];
1485 if (annotation == null)
1489 String displayed = annotation.displayCharacter;
1490 if (displayed == null || displayed.length() != 1)
1494 char symbol = displayed.charAt(0);
1495 if (!Rna.isOpeningParenthesis(symbol))
1501 * found an opening bracket symbol
1502 * count (closing-opening) symbols of this type that follow it,
1503 * up to and excluding the target column; if the count is less
1504 * than 1, the opening bracket is unmatched, so return its match
1506 String closer = String
1507 .valueOf(Rna.getMatchingClosingParenthesis(symbol));
1508 String opener = String.valueOf(symbol);
1510 for (int j = col + 1; j < column; j++)
1512 if (annotations[j] != null)
1514 String s = annotations[j].displayCharacter;
1515 if (closer.equals(s))
1519 else if (opener.equals(s))
1533 protected static synchronized long nextId()
1540 * @return true for rows that have a range of values in their annotation set
1542 public boolean isQuantitative()
1544 return graphMin < graphMax;
1548 * delete any columns in alignmentAnnotation that are hidden (including
1549 * sequence associated annotation).
1551 * @param hiddenColumns
1552 * the set of hidden columns
1554 public void makeVisibleAnnotation(HiddenColumns hiddenColumns)
1556 if (annotations != null)
1558 makeVisibleAnnotation(0, annotations.length, hiddenColumns);
1563 * delete any columns in alignmentAnnotation that are hidden (including
1564 * sequence associated annotation).
1567 * remove any annotation to the right of this column
1569 * remove any annotation to the left of this column
1570 * @param hiddenColumns
1571 * the set of hidden columns
1573 public void makeVisibleAnnotation(int start, int end,
1574 HiddenColumns hiddenColumns)
1576 if (annotations != null)
1578 if (hiddenColumns.hasHiddenColumns())
1580 removeHiddenAnnotation(start, end, hiddenColumns);
1584 restrict(start, end);
1590 * The actual implementation of deleting hidden annotation columns
1593 * remove any annotation to the right of this column
1595 * remove any annotation to the left of this column
1596 * @param hiddenColumns
1597 * the set of hidden columns
1599 private void removeHiddenAnnotation(int start, int end,
1600 HiddenColumns hiddenColumns)
1602 // mangle the alignmentAnnotation annotation array
1603 ArrayList<Annotation[]> annels = new ArrayList<>();
1604 Annotation[] els = null;
1608 Iterator<int[]> blocks = hiddenColumns.getVisContigsIterator(start,
1612 int annotationLength;
1613 while (blocks.hasNext())
1615 int[] block = blocks.next();
1616 annotationLength = block[1] - block[0] + 1;
1618 if (blocks.hasNext())
1620 // copy just the visible segment of the annotation row
1621 copylength = annotationLength;
1625 if (annotationLength + block[0] <= annotations.length)
1627 // copy just the visible segment of the annotation row
1628 copylength = annotationLength;
1632 // copy to the end of the annotation row
1633 copylength = annotations.length - block[0];
1637 els = new Annotation[annotationLength];
1639 System.arraycopy(annotations, block[0], els, 0, copylength);
1640 w += annotationLength;
1645 annotations = new Annotation[w];
1648 for (Annotation[] chnk : annels)
1650 System.arraycopy(chnk, 0, annotations, w, chnk.length);
1656 public static Iterable<AlignmentAnnotation> findAnnotations(
1657 Iterable<AlignmentAnnotation> list, SequenceI seq, String calcId,
1660 ArrayList<AlignmentAnnotation> aa = new ArrayList<>();
1661 for (AlignmentAnnotation ann : list)
1663 if ((calcId == null || (ann.getCalcId() != null
1664 && ann.getCalcId().equals(calcId)))
1665 && (seq == null || (ann.sequenceRef != null
1666 && ann.sequenceRef == seq))
1668 || (ann.label != null && ann.label.equals(label))))
1677 * Answer true if any annotation matches the calcId passed in (if not null).
1680 * annotation to search
1684 public static boolean hasAnnotation(List<AlignmentAnnotation> list,
1688 if (calcId != null && !"".equals(calcId))
1690 for (AlignmentAnnotation a : list)
1692 if (a.getCalcId() == calcId)
1701 public static Iterable<AlignmentAnnotation> findAnnotation(
1702 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)))
1721 public double getBitScore()
1726 public void setBitScore(double bitScore)
1728 this.bitScore = bitScore;
1731 public double getEValue()
1736 public void setEValue(double eValue)
1738 this.eValue = eValue;