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.ArrayList;
24 import java.util.Arrays;
25 import java.util.Collection;
26 import java.util.Collections;
27 import java.util.HashMap;
28 import java.util.Iterator;
29 import java.util.List;
30 import java.util.Locale;
32 import java.util.Map.Entry;
34 import jalview.analysis.Rna;
35 import jalview.analysis.SecStrConsensus.SimpleBP;
36 import jalview.analysis.WUSSParseException;
37 import jalview.structure.StructureImportSettings;
45 public class AlignmentAnnotation
48 private static final String ANNOTATION_ID_PREFIX = "ann";
51 * Identifers for different types of profile data
53 public static final int SEQUENCE_PROFILE = 0;
55 public static final int STRUCTURE_PROFILE = 1;
57 public static final int CDNA_PROFILE = 2;
59 private static long counter = 0;
62 * If true, this annotations is calculated every edit, eg consensus, quality
63 * or conservation graphs
65 public boolean autoCalculated = false;
68 * unique ID for this annotation, used to match up the same annotation row
69 * shown in multiple views and alignments
71 public String annotationId;
74 * the sequence this annotation is associated with (or null)
76 public SequenceI sequenceRef;
78 /** label shown in dropdown menus and in the annotation label area */
81 /** longer description text shown as a tooltip */
82 public String description;
84 /** Array of annotations placed in the current coordinate system */
85 public Annotation[] annotations;
87 public List<SimpleBP> bps = null;
90 * RNA secondary structure contact positions
92 public SequenceFeature[] _rnasecstr = null;
95 * position of annotation resulting in invalid WUSS parsing or -1. -2 means
96 * there was no RNA structure in this annotation
98 private long invalidrnastruc = -2;
101 * the type of temperature factor plot (if it is one)
103 private StructureImportSettings.TFType tfType = StructureImportSettings.TFType.DEFAULT;
105 public void setTFType(StructureImportSettings.TFType t)
110 public StructureImportSettings.TFType getTFType()
116 * Updates the _rnasecstr field Determines the positions that base pair and
117 * the positions of helices based on secondary structure from a Stockholm file
119 * @param rnaAnnotation
121 private void _updateRnaSecStr(CharSequence rnaAnnotation)
125 _rnasecstr = Rna.getHelixMap(rnaAnnotation);
126 invalidrnastruc = -1;
127 } catch (WUSSParseException px)
129 // DEBUG System.out.println(px);
130 invalidrnastruc = px.getProblemPos();
132 if (invalidrnastruc > -1)
137 if (_rnasecstr != null && _rnasecstr.length > 0)
139 // show all the RNA secondary structure annotation symbols.
141 showAllColLabels = true;
142 scaleColLabel = true;
145 // System.out.println("featuregroup " + _rnasecstr[0].getFeatureGroup());
149 private void _markRnaHelices()
152 // Figure out number of helices
153 // Length of rnasecstr is the number of pairs of positions that base pair
154 // with each other in the secondary structure
155 for (int x = 0; x < _rnasecstr.length; x++)
159 * System.out.println(this.annotation._rnasecstr[x] + " Begin" +
160 * this.annotation._rnasecstr[x].getBegin());
162 // System.out.println(this.annotation._rnasecstr[x].getFeatureGroup());
166 val = Integer.valueOf(_rnasecstr[x].getFeatureGroup());
171 } catch (NumberFormatException q)
176 annotations[_rnasecstr[x].getBegin()].value = val;
177 annotations[_rnasecstr[x].getEnd()].value = val;
179 // annotations[_rnasecstr[x].getBegin()].displayCharacter = "" + val;
180 // annotations[_rnasecstr[x].getEnd()].displayCharacter = "" + val;
186 * Get the RNA Secondary Structure SequenceFeature Array if present
188 public SequenceFeature[] getRnaSecondaryStructure()
190 return this._rnasecstr;
194 * Check the RNA Secondary Structure is equivalent to one in given
195 * AlignmentAnnotation param
197 public boolean rnaSecondaryStructureEquivalent(AlignmentAnnotation that)
199 return rnaSecondaryStructureEquivalent(that, true);
202 public boolean rnaSecondaryStructureEquivalent(AlignmentAnnotation that,
205 SequenceFeature[] thisSfArray = this.getRnaSecondaryStructure();
206 SequenceFeature[] thatSfArray = that.getRnaSecondaryStructure();
207 if (thisSfArray == null || thatSfArray == null)
209 return thisSfArray == null && thatSfArray == null;
211 if (thisSfArray.length != thatSfArray.length)
215 Arrays.sort(thisSfArray, new SFSortByEnd()); // probably already sorted
217 Arrays.sort(thatSfArray, new SFSortByEnd()); // probably already sorted
219 for (int i = 0; i < thisSfArray.length; i++)
221 SequenceFeature thisSf = thisSfArray[i];
222 SequenceFeature thatSf = thatSfArray[i];
225 if (thisSf.getType() == null || thatSf.getType() == null)
227 if (thisSf.getType() == null && thatSf.getType() == null)
236 if (!thisSf.getType().equals(thatSf.getType()))
241 if (!(thisSf.getBegin() == thatSf.getBegin()
242 && thisSf.getEnd() == thatSf.getEnd()))
252 * map of positions in the associated annotation
254 private Map<Integer, Annotation> sequenceMapping;
257 * lower range for quantitative data
259 public float graphMin;
262 * Upper range for quantitative data
264 public float graphMax;
267 * Score associated with label and description.
269 public double score = Double.NaN;
272 * flag indicating if annotation has a score.
274 public boolean hasScore = false;
276 public GraphLine threshold;
278 // Graphical hints and tips
280 /** Can this row be edited by the user ? */
281 public boolean editable = false;
283 /** Indicates if annotation has a graphical symbol track */
284 public boolean hasIcons; //
286 /** Indicates if annotation has a text character label */
287 public boolean hasText;
289 /** is the row visible */
290 public boolean visible = true;
292 public int graphGroup = -1;
294 /** Displayed height of row in pixels */
295 public int height = 0;
297 public int graph = 0;
299 public int graphHeight = 40;
301 public boolean padGaps = false;
303 public static final int NO_GRAPH = 0;
305 public static final int BAR_GRAPH = 1;
307 public static final int LINE_GRAPH = 2;
309 public static final int CONTACT_MAP = 4;
311 public boolean belowAlignment = true;
313 public SequenceGroup groupRef = null;
316 * display every column label, even if there is a row of identical labels
318 public boolean showAllColLabels = false;
321 * scale the column label to fit within the alignment column.
323 public boolean scaleColLabel = false;
326 * centre the column labels relative to the alignment column
328 public boolean centreColLabels = false;
330 private boolean isrna;
332 public static int getGraphValueFromString(String string)
334 if (string.equalsIgnoreCase("BAR_GRAPH"))
338 else if (string.equalsIgnoreCase("LINE_GRAPH"))
349 * Creates a new AlignmentAnnotation object.
352 * short label shown under sequence labels
354 * text displayed on mouseover
356 * set of positional annotation elements
358 public AlignmentAnnotation(String label, String description,
359 Annotation[] annotations)
365 this.description = description;
366 this.annotations = annotations;
368 validateRangeAndDisplay();
372 * Checks if annotation labels represent secondary structures
375 void areLabelsSecondaryStructure()
377 boolean nonSSLabel = false;
379 StringBuffer rnastring = new StringBuffer();
382 for (int i = 0; i < annotations.length; i++)
384 // DEBUG System.out.println(i + ": " + annotations[i]);
385 if (annotations[i] == null)
389 if (annotations[i].secondaryStructure == 'H'
390 || annotations[i].secondaryStructure == 'E')
392 // DEBUG System.out.println( "/H|E/ '" +
393 // annotations[i].secondaryStructure + "'");
397 // Check for RNA secondary structure
399 // DEBUG System.out.println( "/else/ '" +
400 // annotations[i].secondaryStructure + "'");
401 // TODO: 2.8.2 should this ss symbol validation check be a function in
402 // RNA/ResidueProperties ?
403 // allow for DSSP extended code:
404 // https://www.wikidoc.org/index.php/Secondary_structure#The_DSSP_code
405 // GHITEBS as well as C and X (for missing?)
406 if (annotations[i].secondaryStructure == '('
407 || annotations[i].secondaryStructure == '['
408 || annotations[i].secondaryStructure == '<'
409 || annotations[i].secondaryStructure == '{'
410 || annotations[i].secondaryStructure == 'A'
411 // || annotations[i].secondaryStructure == 'B'
412 // || annotations[i].secondaryStructure == 'C'
413 || annotations[i].secondaryStructure == 'D'
414 // || annotations[i].secondaryStructure == 'E' // ambiguous on
415 // its own -- already checked above
416 || annotations[i].secondaryStructure == 'F'
417 // || annotations[i].secondaryStructure == 'G'
418 // || annotations[i].secondaryStructure == 'H' // ambiguous on
419 // its own -- already checked above
420 // || annotations[i].secondaryStructure == 'I'
421 || annotations[i].secondaryStructure == 'J'
422 || annotations[i].secondaryStructure == 'K'
423 || annotations[i].secondaryStructure == 'L'
424 || annotations[i].secondaryStructure == 'M'
425 || annotations[i].secondaryStructure == 'N'
426 || annotations[i].secondaryStructure == 'O'
427 || annotations[i].secondaryStructure == 'P'
428 || annotations[i].secondaryStructure == 'Q'
429 || annotations[i].secondaryStructure == 'R'
430 // || annotations[i].secondaryStructure == 'S'
431 // || annotations[i].secondaryStructure == 'T'
432 || annotations[i].secondaryStructure == 'U'
433 || annotations[i].secondaryStructure == 'V'
434 || annotations[i].secondaryStructure == 'W'
435 // || annotations[i].secondaryStructure == 'X'
436 || annotations[i].secondaryStructure == 'Y'
437 || annotations[i].secondaryStructure == 'Z')
444 // System.out.println("displaychar " + annotations[i].displayCharacter);
446 if (annotations[i].displayCharacter == null
447 || annotations[i].displayCharacter.length() == 0)
449 rnastring.append('.');
452 if (annotations[i].displayCharacter.length() == 1)
454 firstChar = annotations[i].displayCharacter.charAt(0);
455 // check to see if it looks like a sequence or is secondary structure
457 if (annotations[i].secondaryStructure != ' ' && !hasIcons &&
458 // Uncomment to only catch case where
459 // displayCharacter==secondary
461 // to correctly redisplay SS annotation imported from Stockholm,
462 // exported to JalviewXML and read back in again.
464 // annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure
465 firstChar != ' ' && firstChar != '$' && firstChar != 0xCE
466 && firstChar != '(' && firstChar != '[' && firstChar != '<'
467 && firstChar != '{' && firstChar != 'A' && firstChar != 'B'
468 && firstChar != 'C' && firstChar != 'D' && firstChar != 'E'
469 && firstChar != 'F' && firstChar != 'G' && firstChar != 'H'
470 && firstChar != 'I' && firstChar != 'J' && firstChar != 'K'
471 && firstChar != 'L' && firstChar != 'M' && firstChar != 'N'
472 && firstChar != 'O' && firstChar != 'P' && firstChar != 'Q'
473 && firstChar != 'R' && firstChar != 'S' && firstChar != 'T'
474 && firstChar != 'U' && firstChar != 'V' && firstChar != 'W'
475 && firstChar != 'X' && firstChar != 'Y' && firstChar != 'Z'
477 && firstChar < jalview.schemes.ResidueProperties.aaIndex.length)
479 if (jalview.schemes.ResidueProperties.aaIndex[firstChar] < 23) // TODO:
492 rnastring.append(annotations[i].displayCharacter.charAt(1));
495 if (annotations[i].displayCharacter.length() > 0)
504 for (int j = 0; j < annotations.length; j++)
506 if (annotations[j] != null
507 && annotations[j].secondaryStructure != ' ')
509 annotations[j].displayCharacter = String
510 .valueOf(annotations[j].secondaryStructure);
511 annotations[j].secondaryStructure = ' ';
520 _updateRnaSecStr(new AnnotCharSequence());
526 * flyweight access to positions in the alignment annotation row for RNA
532 private class AnnotCharSequence implements CharSequence
538 public AnnotCharSequence()
540 this(0, annotations.length);
543 AnnotCharSequence(int start, int end)
550 public CharSequence subSequence(int start, int end)
552 return new AnnotCharSequence(offset + start, offset + end);
562 public char charAt(int index)
564 return ((index + offset < 0) || (index + offset) >= max
565 || annotations[index + offset] == null
566 || (annotations[index + offset].secondaryStructure <= ' ')
568 : annotations[index + offset].displayCharacter == null
570 + offset].displayCharacter
573 + offset].secondaryStructure
575 + offset].displayCharacter
580 public String toString()
582 char[] string = new char[max - offset];
583 int mx = annotations.length;
585 for (int i = offset; i < mx; i++)
587 string[i] = (annotations[i] == null
588 || (annotations[i].secondaryStructure <= 32))
590 : (annotations[i].displayCharacter == null
591 || annotations[i].displayCharacter
593 ? annotations[i].secondaryStructure
594 : annotations[i].displayCharacter
597 return new String(string);
601 private long _lastrnaannot = -1;
603 public String getRNAStruc()
607 String rnastruc = new AnnotCharSequence().toString();
608 if (_lastrnaannot != rnastruc.hashCode())
610 // ensure rna structure contacts are up to date
611 _lastrnaannot = rnastruc.hashCode();
612 _updateRnaSecStr(rnastruc);
620 * Creates a new AlignmentAnnotation object.
635 public AlignmentAnnotation(String label, String description,
636 Annotation[] annotations, float min, float max, int graphType)
639 // graphs are not editable
640 editable = graphType == 0;
643 this.description = description;
644 this.annotations = annotations;
648 validateRangeAndDisplay();
652 * checks graphMin and graphMax, secondary structure symbols, sets graphType
653 * appropriately, sets null labels to the empty string if appropriate.
655 public void validateRangeAndDisplay()
658 if (annotations == null)
660 visible = false; // try to prevent renderer from displaying.
661 invalidrnastruc = -1;
662 return; // this is a non-annotation row annotation - ie a sequence score.
665 int graphType = graph;
666 float min = graphMin;
667 float max = graphMax;
668 boolean drawValues = true;
673 for (int i = 0; i < annotations.length; i++)
675 if (annotations[i] == null)
680 if (drawValues && annotations[i].displayCharacter != null
681 && annotations[i].displayCharacter.length() > 1)
686 if (annotations[i].value > max)
688 max = annotations[i].value;
691 if (annotations[i].value < min)
693 min = annotations[i].value;
695 if (_linecolour == null && annotations[i].colour != null)
697 _linecolour = annotations[i].colour;
700 // ensure zero is origin for min/max ranges on only one side of zero
717 areLabelsSecondaryStructure();
719 if (!drawValues && graphType != NO_GRAPH)
721 for (int i = 0; i < annotations.length; i++)
723 if (annotations[i] != null)
725 annotations[i].displayCharacter = "";
732 * Copy constructor creates a new independent annotation row with the same
733 * associated sequenceRef
737 public AlignmentAnnotation(AlignmentAnnotation annotation)
740 this.label = new String(annotation.label);
741 if (annotation.description != null)
743 this.description = new String(annotation.description);
745 this.graphMin = annotation.graphMin;
746 this.graphMax = annotation.graphMax;
747 this.graph = annotation.graph;
748 this.graphHeight = annotation.graphHeight;
749 this.graphGroup = annotation.graphGroup;
750 this.groupRef = annotation.groupRef;
751 this.editable = annotation.editable;
752 this.autoCalculated = annotation.autoCalculated;
753 this.hasIcons = annotation.hasIcons;
754 this.hasText = annotation.hasText;
755 this.height = annotation.height;
756 this.label = annotation.label;
757 this.padGaps = annotation.padGaps;
758 this.visible = annotation.visible;
759 this.centreColLabels = annotation.centreColLabels;
760 this.scaleColLabel = annotation.scaleColLabel;
761 this.showAllColLabels = annotation.showAllColLabels;
762 this.calcId = annotation.calcId;
763 if (annotation.properties != null)
765 properties = new HashMap<>();
766 for (Map.Entry<String, String> val : annotation.properties.entrySet())
768 properties.put(val.getKey(), val.getValue());
771 if (this.hasScore = annotation.hasScore)
773 this.score = annotation.score;
775 if (annotation.threshold != null)
777 threshold = new GraphLine(annotation.threshold);
779 Annotation[] ann = annotation.annotations;
780 if (annotation.annotations != null)
782 this.annotations = new Annotation[ann.length];
783 for (int i = 0; i < ann.length; i++)
787 annotations[i] = new Annotation(ann[i]);
788 if (_linecolour != null)
790 _linecolour = annotations[i].colour;
795 if (annotation.sequenceRef != null)
797 this.sequenceRef = annotation.sequenceRef;
798 if (annotation.sequenceMapping != null)
801 sequenceMapping = new HashMap<>();
802 Iterator<Integer> pos = annotation.sequenceMapping.keySet()
804 while (pos.hasNext())
806 // could optimise this!
808 Annotation a = annotation.sequenceMapping.get(p);
815 for (int i = 0; i < ann.length; i++)
819 sequenceMapping.put(p, annotations[i]);
827 this.sequenceMapping = null;
831 // TODO: check if we need to do this: JAL-952
832 // if (this.isrna=annotation.isrna)
834 // _rnasecstr=new SequenceFeature[annotation._rnasecstr];
836 validateRangeAndDisplay(); // construct hashcodes, etc.
840 * clip the annotation to the columns given by startRes and endRes (inclusive)
841 * and prune any existing sequenceMapping to just those columns.
846 public void restrict(int startRes, int endRes)
848 if (annotations == null)
857 if (startRes >= annotations.length)
859 startRes = annotations.length - 1;
861 if (endRes >= annotations.length)
863 endRes = annotations.length - 1;
865 if (annotations == null)
869 Annotation[] temp = new Annotation[endRes - startRes + 1];
870 if (startRes < annotations.length)
872 System.arraycopy(annotations, startRes, temp, 0,
873 endRes - startRes + 1);
875 if (sequenceRef != null)
877 // Clip the mapping, if it exists.
878 int spos = sequenceRef.findPosition(startRes);
879 int epos = sequenceRef.findPosition(endRes);
880 if (sequenceMapping != null)
882 Map<Integer, Annotation> newmapping = new HashMap<>();
883 Iterator<Integer> e = sequenceMapping.keySet().iterator();
886 Integer pos = e.next();
887 if (pos.intValue() >= spos && pos.intValue() <= epos)
889 newmapping.put(pos, sequenceMapping.get(pos));
892 sequenceMapping.clear();
893 sequenceMapping = newmapping;
900 * set the annotation row to be at least length Annotations
903 * minimum number of columns required in the annotation row
904 * @return false if the annotation row is greater than length
906 public boolean padAnnotation(int length)
908 if (annotations == null)
910 return true; // annotation row is correct - null == not visible and
913 if (annotations.length < length)
915 Annotation[] na = new Annotation[length];
916 System.arraycopy(annotations, 0, na, 0, annotations.length);
920 return annotations.length > length;
927 * @return DOCUMENT ME!
930 public String toString()
932 if (annotations == null)
936 StringBuilder buffer = new StringBuilder(256);
938 for (int i = 0; i < annotations.length; i++)
940 if (annotations[i] != null)
944 buffer.append(annotations[i].value);
948 buffer.append(annotations[i].secondaryStructure);
952 buffer.append(annotations[i].displayCharacter);
958 // TODO: remove disgusting hack for 'special' treatment of consensus line.
959 if (label.indexOf("Consensus") == 0)
963 for (int i = 0; i < annotations.length; i++)
965 if (annotations[i] != null)
967 buffer.append(annotations[i].description);
974 return buffer.toString();
977 public void setThreshold(GraphLine line)
982 public GraphLine getThreshold()
988 * Attach the annotation to seqRef, starting from startRes position. If
989 * alreadyMapped is true then the indices of the annotation[] array are
990 * sequence positions rather than alignment column positions.
994 * @param alreadyMapped
996 public void createSequenceMapping(SequenceI seqRef, int startRes,
997 boolean alreadyMapped)
1004 sequenceRef = seqRef;
1005 if (annotations == null)
1009 sequenceMapping = new HashMap<>();
1013 for (int i = 0; i < annotations.length; i++)
1015 if (annotations[i] != null)
1019 seqPos = seqRef.findPosition(i);
1023 seqPos = i + startRes;
1026 sequenceMapping.put(Integer.valueOf(seqPos), annotations[i]);
1033 * When positional annotation and a sequence reference is present, clears and
1034 * resizes the annotations array to the current alignment width, and adds
1035 * annotation according to aligned positions of the sequenceRef given by
1038 public void adjustForAlignment()
1040 if (sequenceRef == null)
1045 if (annotations == null)
1050 int a = 0, aSize = sequenceRef.getLength();
1059 Annotation[] temp = new Annotation[aSize];
1061 if (sequenceMapping != null)
1063 for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++)
1065 index = Integer.valueOf(a);
1066 Annotation annot = sequenceMapping.get(index);
1069 position = sequenceRef.findIndex(a) - 1;
1071 temp[position] = annot;
1079 * remove any null entries in annotation row and return the number of non-null
1080 * annotation elements.
1084 public int compactAnnotationArray()
1086 int i = 0, iSize = annotations.length;
1089 if (annotations[i] == null)
1093 System.arraycopy(annotations, i + 1, annotations, i,
1103 Annotation[] ann = annotations;
1104 annotations = new Annotation[i];
1105 System.arraycopy(ann, 0, annotations, 0, i);
1111 * Associate this annotation with the aligned residues of a particular
1112 * sequence. sequenceMapping will be updated in the following way: null
1113 * sequenceI - existing mapping will be discarded but annotations left in
1114 * mapped positions. valid sequenceI not equal to current sequenceRef: mapping
1115 * is discarded and rebuilt assuming 1:1 correspondence TODO: overload with
1116 * parameter to specify correspondence between current and new sequenceRef
1120 public void setSequenceRef(SequenceI sequenceI)
1122 if (sequenceI != null)
1124 if (sequenceRef != null)
1126 boolean rIsDs = sequenceRef.getDatasetSequence() == null,
1127 tIsDs = sequenceI.getDatasetSequence() == null;
1128 if (sequenceRef != sequenceI
1130 && sequenceRef != sequenceI.getDatasetSequence())
1132 && sequenceRef.getDatasetSequence() != sequenceI)
1133 && (!rIsDs && !tIsDs
1134 && sequenceRef.getDatasetSequence() != sequenceI
1135 .getDatasetSequence())
1136 && !sequenceRef.equals(sequenceI))
1138 // if sequenceRef isn't intersecting with sequenceI
1139 // throw away old mapping and reconstruct.
1141 if (sequenceMapping != null)
1143 sequenceMapping = null;
1144 // compactAnnotationArray();
1146 createSequenceMapping(sequenceI, 1, true);
1147 adjustForAlignment();
1151 // Mapping carried over
1152 sequenceRef = sequenceI;
1157 // No mapping exists
1158 createSequenceMapping(sequenceI, 1, true);
1159 adjustForAlignment();
1164 // throw away the mapping without compacting.
1165 sequenceMapping = null;
1173 public double getScore()
1182 public void setScore(double score)
1190 * @return true if annotation has an associated score
1192 public boolean hasScore()
1194 return hasScore || !Double.isNaN(score);
1198 * Score only annotation
1201 * @param description
1204 public AlignmentAnnotation(String label, String description, double score)
1206 this(label, description, null);
1211 * copy constructor with edit based on the hidden columns marked in colSel
1213 * @param alignmentAnnotation
1216 public AlignmentAnnotation(AlignmentAnnotation alignmentAnnotation,
1217 HiddenColumns hidden)
1219 this(alignmentAnnotation);
1220 if (annotations == null)
1224 makeVisibleAnnotation(hidden);
1227 public void setPadGaps(boolean padgaps, char gapchar)
1229 this.padGaps = padgaps;
1233 for (int i = 0; i < annotations.length; i++)
1235 if (annotations[i] == null)
1237 annotations[i] = new Annotation(String.valueOf(gapchar), null,
1240 else if (annotations[i].displayCharacter == null
1241 || annotations[i].displayCharacter.equals(" "))
1243 annotations[i].displayCharacter = String.valueOf(gapchar);
1250 * format description string for display
1253 * @return Get the annotation description string optionally prefixed by
1254 * associated sequence name (if any)
1256 public String getDescription(boolean seqname)
1258 if (seqname && this.sequenceRef != null)
1260 int i = description.toLowerCase(Locale.ROOT).indexOf("<html>");
1263 // move the html tag to before the sequence reference.
1264 return "<html>" + sequenceRef.getName() + " : "
1265 + description.substring(i + 6);
1267 return sequenceRef.getName() + " : " + description;
1272 public boolean isValidStruc()
1274 return invalidrnastruc == -1;
1277 public long getInvalidStrucPos()
1279 return invalidrnastruc;
1283 * machine readable ID string indicating what generated this annotation
1285 protected String calcId = "";
1288 * properties associated with the calcId
1290 protected Map<String, String> properties = new HashMap<>();
1293 * base colour for line graphs. If null, will be set automatically by
1294 * searching the alignment annotation
1296 public java.awt.Color _linecolour;
1298 public String getCalcId()
1303 public void setCalcId(String calcId)
1305 this.calcId = calcId;
1308 public boolean isRNA()
1314 * transfer annotation to the given sequence using the given mapping from the
1315 * current positions or an existing sequence mapping
1319 * map involving sq as To or From
1321 public void liftOver(SequenceI sq, Mapping sp2sq)
1323 if (sp2sq.getMappedWidth() != sp2sq.getWidth())
1325 // TODO: employ getWord/MappedWord to transfer annotation between cDNA and
1326 // Protein reference frames
1328 "liftOver currently not implemented for transfer of annotation between different types of seqeunce");
1330 boolean mapIsTo = (sp2sq != null)
1331 ? (sp2sq.getTo() == sq
1332 || sp2sq.getTo() == sq.getDatasetSequence())
1335 // TODO build a better annotation element map and get rid of annotations[]
1336 Map<Integer, Annotation> mapForsq = new HashMap<>();
1337 if (sequenceMapping != null)
1341 for (Entry<Integer, Annotation> ie : sequenceMapping.entrySet())
1343 Integer mpos = Integer
1344 .valueOf(mapIsTo ? sp2sq.getMappedPosition(ie.getKey())
1345 : sp2sq.getPosition(ie.getKey()));
1346 if (mpos >= sq.getStart() && mpos <= sq.getEnd())
1348 mapForsq.put(mpos, ie.getValue());
1351 sequenceMapping = mapForsq;
1353 adjustForAlignment();
1363 * like liftOver but more general.
1365 * Takes an array of int pairs that will be used to update the internal
1366 * sequenceMapping and so shuffle the annotated positions
1369 * - new sequence reference for the annotation row - if null,
1370 * sequenceRef is left unchanged
1372 * array of ints containing corresponding positions
1374 * - column for current coordinate system (-1 for index+1)
1376 * - column for destination coordinate system (-1 for index+1)
1378 * - offset added to index when referencing either coordinate system
1379 * @note no checks are made as to whether from and/or to are sensible
1380 * @note caller should add the remapped annotation to newref if they have not
1383 public void remap(SequenceI newref, HashMap<Integer, int[]> mapping,
1384 int from, int to, int idxoffset)
1386 if (mapping != null)
1388 Map<Integer, Annotation> old = sequenceMapping;
1389 Map<Integer, Annotation> remap = new HashMap<>();
1391 for (int mp[] : mapping.values())
1397 Annotation ann = null;
1400 ann = sequenceMapping.get(Integer.valueOf(idxoffset + index));
1404 if (mp != null && mp.length > from)
1406 ann = sequenceMapping.get(Integer.valueOf(mp[from]));
1413 remap.put(Integer.valueOf(idxoffset + index), ann);
1417 if (to > -1 && to < mp.length)
1419 remap.put(Integer.valueOf(mp[to]), ann);
1424 sequenceMapping = remap;
1428 sequenceRef = newref;
1430 adjustForAlignment();
1434 public String getProperty(String property)
1436 if (properties == null)
1440 return properties.get(property);
1443 public void setProperty(String property, String value)
1445 if (properties == null)
1447 properties = new HashMap<>();
1449 properties.put(property, value);
1452 public boolean hasProperties()
1454 return properties != null && properties.size() > 0;
1457 public Collection<String> getProperties()
1459 if (properties == null)
1461 return Collections.emptyList();
1463 return properties.keySet();
1467 * Returns the Annotation for the given sequence position (base 1) if any,
1473 public Annotation getAnnotationForPosition(int position)
1475 return sequenceMapping == null ? null : sequenceMapping.get(position);
1480 * Set the id to "ann" followed by a counter that increments so as to be
1481 * unique for the lifetime of the JVM
1483 protected final void setAnnotationId()
1485 this.annotationId = ANNOTATION_ID_PREFIX + Long.toString(nextId());
1489 * Returns the match for the last unmatched opening RNA helix pair symbol
1490 * preceding the given column, or '(' if nothing found to match.
1495 public String getDefaultRnaHelixSymbol(int column)
1497 String result = "(";
1498 if (annotations == null)
1504 * for each preceding column, if it contains an open bracket,
1505 * count whether it is still unmatched at column, if so return its pair
1506 * (likely faster than the fancy alternative using stacks)
1508 for (int col = column - 1; col >= 0; col--)
1510 Annotation annotation = annotations[col];
1511 if (annotation == null)
1515 String displayed = annotation.displayCharacter;
1516 if (displayed == null || displayed.length() != 1)
1520 char symbol = displayed.charAt(0);
1521 if (!Rna.isOpeningParenthesis(symbol))
1527 * found an opening bracket symbol
1528 * count (closing-opening) symbols of this type that follow it,
1529 * up to and excluding the target column; if the count is less
1530 * than 1, the opening bracket is unmatched, so return its match
1532 String closer = String
1533 .valueOf(Rna.getMatchingClosingParenthesis(symbol));
1534 String opener = String.valueOf(symbol);
1536 for (int j = col + 1; j < column; j++)
1538 if (annotations[j] != null)
1540 String s = annotations[j].displayCharacter;
1541 if (closer.equals(s))
1545 else if (opener.equals(s))
1559 protected static synchronized long nextId()
1566 * @return true for rows that have a range of values in their annotation set
1568 public boolean isQuantitative()
1570 return graphMin < graphMax;
1574 * delete any columns in alignmentAnnotation that are hidden (including
1575 * sequence associated annotation).
1577 * @param hiddenColumns
1578 * the set of hidden columns
1580 public void makeVisibleAnnotation(HiddenColumns hiddenColumns)
1582 if (annotations != null)
1584 makeVisibleAnnotation(0, annotations.length, hiddenColumns);
1589 * delete any columns in alignmentAnnotation that are hidden (including
1590 * sequence associated annotation).
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 public void makeVisibleAnnotation(int start, int end,
1600 HiddenColumns hiddenColumns)
1602 if (annotations != null)
1604 if (hiddenColumns.hasHiddenColumns())
1606 removeHiddenAnnotation(start, end, hiddenColumns);
1610 restrict(start, end);
1616 * The actual implementation of deleting hidden annotation columns
1619 * remove any annotation to the right of this column
1621 * remove any annotation to the left of this column
1622 * @param hiddenColumns
1623 * the set of hidden columns
1625 private void removeHiddenAnnotation(int start, int end,
1626 HiddenColumns hiddenColumns)
1628 // mangle the alignmentAnnotation annotation array
1629 ArrayList<Annotation[]> annels = new ArrayList<>();
1630 Annotation[] els = null;
1634 Iterator<int[]> blocks = hiddenColumns.getVisContigsIterator(start,
1638 int annotationLength;
1639 while (blocks.hasNext())
1641 int[] block = blocks.next();
1642 annotationLength = block[1] - block[0] + 1;
1644 if (blocks.hasNext())
1646 // copy just the visible segment of the annotation row
1647 copylength = annotationLength;
1651 if (annotationLength + block[0] <= annotations.length)
1653 // copy just the visible segment of the annotation row
1654 copylength = annotationLength;
1658 // copy to the end of the annotation row
1659 copylength = annotations.length - block[0];
1663 els = new Annotation[annotationLength];
1665 System.arraycopy(annotations, block[0], els, 0, copylength);
1666 w += annotationLength;
1671 annotations = new Annotation[w];
1674 for (Annotation[] chnk : annels)
1676 System.arraycopy(chnk, 0, annotations, w, chnk.length);
1682 public static Iterable<AlignmentAnnotation> findAnnotations(
1683 Iterable<AlignmentAnnotation> list, SequenceI seq, String calcId,
1687 ArrayList<AlignmentAnnotation> aa = new ArrayList<>();
1688 for (AlignmentAnnotation ann : list)
1690 if ((calcId == null || (ann.getCalcId() != null
1691 && ann.getCalcId().equals(calcId)))
1692 && (seq == null || (ann.sequenceRef != null
1693 && ann.sequenceRef == seq))
1695 || (ann.label != null && ann.label.equals(label))))
1704 * Answer true if any annotation matches the calcId passed in (if not null).
1707 * annotation to search
1711 public static boolean hasAnnotation(List<AlignmentAnnotation> list,
1715 if (calcId != null && !"".equals(calcId))
1717 for (AlignmentAnnotation a : list)
1719 if (a.getCalcId() == calcId)
1728 public static Iterable<AlignmentAnnotation> findAnnotation(
1729 List<AlignmentAnnotation> list, String calcId)
1732 List<AlignmentAnnotation> aa = new ArrayList<>();
1737 for (AlignmentAnnotation a : list)
1740 if (a.getCalcId() == calcId || (a.getCalcId() != null
1741 && calcId != null && a.getCalcId().equals(calcId)))