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 jalview.bin.Console.outPrintln(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 // jalview.bin.Console.outPrintln("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 * jalview.bin.Console.outPrintln(this.annotation._rnasecstr[x] + " Begin" +
160 * this.annotation._rnasecstr[x].getBegin());
162 // jalview.bin.Console.outPrintln(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;
312 * property that when set to non-empty string disables display of column groups defined on the contact matrix
314 public static final String CONTACT_MAP_NOGROUPS = "CMNOGRPS";
316 public boolean belowAlignment = true;
318 public SequenceGroup groupRef = null;
321 * display every column label, even if there is a row of identical labels
323 public boolean showAllColLabels = false;
326 * scale the column label to fit within the alignment column.
328 public boolean scaleColLabel = false;
331 * centre the column labels relative to the alignment column
333 public boolean centreColLabels = false;
335 private boolean isrna;
337 public static int getGraphValueFromString(String string)
339 if (string.equalsIgnoreCase("BAR_GRAPH"))
343 else if (string.equalsIgnoreCase("LINE_GRAPH"))
354 * Creates a new AlignmentAnnotation object.
357 * short label shown under sequence labels
359 * text displayed on mouseover
361 * set of positional annotation elements
363 public AlignmentAnnotation(String label, String description,
364 Annotation[] annotations)
370 this.description = description;
371 this.annotations = annotations;
373 validateRangeAndDisplay();
377 * Checks if annotation labels represent secondary structures
380 void areLabelsSecondaryStructure()
382 boolean nonSSLabel = false;
384 StringBuffer rnastring = new StringBuffer();
387 for (int i = 0; i < annotations.length; i++)
389 // DEBUG jalview.bin.Console.outPrintln(i + ": " + annotations[i]);
390 if (annotations[i] == null)
394 if (annotations[i].secondaryStructure == 'H'
395 || annotations[i].secondaryStructure == 'E')
397 // DEBUG jalview.bin.Console.outPrintln( "/H|E/ '" +
398 // annotations[i].secondaryStructure + "'");
402 // Check for RNA secondary structure
404 // DEBUG jalview.bin.Console.outPrintln( "/else/ '" +
405 // annotations[i].secondaryStructure + "'");
406 // TODO: 2.8.2 should this ss symbol validation check be a function in
407 // RNA/ResidueProperties ?
408 // allow for DSSP extended code:
409 // https://www.wikidoc.org/index.php/Secondary_structure#The_DSSP_code
410 // GHITEBS as well as C and X (for missing?)
411 if (annotations[i].secondaryStructure == '('
412 || annotations[i].secondaryStructure == '['
413 || annotations[i].secondaryStructure == '<'
414 || annotations[i].secondaryStructure == '{'
415 || annotations[i].secondaryStructure == 'A'
416 // || annotations[i].secondaryStructure == 'B'
417 // || annotations[i].secondaryStructure == 'C'
418 || annotations[i].secondaryStructure == 'D'
419 // || annotations[i].secondaryStructure == 'E' // ambiguous on
420 // its own -- already checked above
421 || annotations[i].secondaryStructure == 'F'
422 // || annotations[i].secondaryStructure == 'G'
423 // || annotations[i].secondaryStructure == 'H' // ambiguous on
424 // its own -- already checked above
425 // || annotations[i].secondaryStructure == 'I'
426 || annotations[i].secondaryStructure == 'J'
427 || annotations[i].secondaryStructure == 'K'
428 || annotations[i].secondaryStructure == 'L'
429 || annotations[i].secondaryStructure == 'M'
430 || annotations[i].secondaryStructure == 'N'
431 || annotations[i].secondaryStructure == 'O'
432 || annotations[i].secondaryStructure == 'P'
433 || annotations[i].secondaryStructure == 'Q'
434 || annotations[i].secondaryStructure == 'R'
435 // || annotations[i].secondaryStructure == 'S'
436 // || annotations[i].secondaryStructure == 'T'
437 || annotations[i].secondaryStructure == 'U'
438 || annotations[i].secondaryStructure == 'V'
439 || annotations[i].secondaryStructure == 'W'
440 // || annotations[i].secondaryStructure == 'X'
441 || annotations[i].secondaryStructure == 'Y'
442 || annotations[i].secondaryStructure == 'Z')
449 // jalview.bin.Console.outPrintln("displaychar " + annotations[i].displayCharacter);
451 if (annotations[i].displayCharacter == null
452 || annotations[i].displayCharacter.length() == 0)
454 rnastring.append('.');
457 if (annotations[i].displayCharacter.length() == 1)
459 firstChar = annotations[i].displayCharacter.charAt(0);
460 // check to see if it looks like a sequence or is secondary structure
462 if (annotations[i].secondaryStructure != ' ' && !hasIcons &&
463 // Uncomment to only catch case where
464 // displayCharacter==secondary
466 // to correctly redisplay SS annotation imported from Stockholm,
467 // exported to JalviewXML and read back in again.
469 // annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure
470 firstChar != ' ' && firstChar != '$' && firstChar != 0xCE
471 && firstChar != '(' && firstChar != '[' && firstChar != '<'
472 && firstChar != '{' && firstChar != 'A' && firstChar != 'B'
473 && firstChar != 'C' && firstChar != 'D' && firstChar != 'E'
474 && firstChar != 'F' && firstChar != 'G' && firstChar != 'H'
475 && firstChar != 'I' && firstChar != 'J' && firstChar != 'K'
476 && firstChar != 'L' && firstChar != 'M' && firstChar != 'N'
477 && firstChar != 'O' && firstChar != 'P' && firstChar != 'Q'
478 && firstChar != 'R' && firstChar != 'S' && firstChar != 'T'
479 && firstChar != 'U' && firstChar != 'V' && firstChar != 'W'
480 && firstChar != 'X' && firstChar != 'Y' && firstChar != 'Z'
482 && firstChar < jalview.schemes.ResidueProperties.aaIndex.length)
484 if (jalview.schemes.ResidueProperties.aaIndex[firstChar] < 23) // TODO:
497 rnastring.append(annotations[i].displayCharacter.charAt(1));
500 if (annotations[i].displayCharacter.length() > 0)
509 for (int j = 0; j < annotations.length; j++)
511 if (annotations[j] != null
512 && annotations[j].secondaryStructure != ' ')
514 annotations[j].displayCharacter = String
515 .valueOf(annotations[j].secondaryStructure);
516 annotations[j].secondaryStructure = ' ';
525 _updateRnaSecStr(new AnnotCharSequence());
531 * flyweight access to positions in the alignment annotation row for RNA
537 private class AnnotCharSequence implements CharSequence
543 public AnnotCharSequence()
545 this(0, annotations.length);
548 AnnotCharSequence(int start, int end)
555 public CharSequence subSequence(int start, int end)
557 return new AnnotCharSequence(offset + start, offset + end);
567 public char charAt(int index)
569 return ((index + offset < 0) || (index + offset) >= max
570 || annotations[index + offset] == null
571 || (annotations[index + offset].secondaryStructure <= ' ')
573 : annotations[index + offset].displayCharacter == null
575 + offset].displayCharacter
578 + offset].secondaryStructure
580 + offset].displayCharacter
585 public String toString()
587 char[] string = new char[max - offset];
588 int mx = annotations.length;
590 for (int i = offset; i < mx; i++)
592 string[i] = (annotations[i] == null
593 || (annotations[i].secondaryStructure <= 32))
595 : (annotations[i].displayCharacter == null
596 || annotations[i].displayCharacter
598 ? annotations[i].secondaryStructure
599 : annotations[i].displayCharacter
602 return new String(string);
606 private long _lastrnaannot = -1;
608 public String getRNAStruc()
612 String rnastruc = new AnnotCharSequence().toString();
613 if (_lastrnaannot != rnastruc.hashCode())
615 // ensure rna structure contacts are up to date
616 _lastrnaannot = rnastruc.hashCode();
617 _updateRnaSecStr(rnastruc);
625 * Creates a new AlignmentAnnotation object.
640 public AlignmentAnnotation(String label, String description,
641 Annotation[] annotations, float min, float max, int graphType)
644 // graphs are not editable
645 editable = graphType == 0;
648 this.description = description;
649 this.annotations = annotations;
653 validateRangeAndDisplay();
657 * checks graphMin and graphMax, secondary structure symbols, sets graphType
658 * appropriately, sets null labels to the empty string if appropriate.
660 public void validateRangeAndDisplay()
663 if (annotations == null)
665 visible = false; // try to prevent renderer from displaying.
666 invalidrnastruc = -1;
667 return; // this is a non-annotation row annotation - ie a sequence score.
670 int graphType = graph;
671 float min = graphMin;
672 float max = graphMax;
673 boolean drawValues = true;
678 for (int i = 0; i < annotations.length; i++)
680 if (annotations[i] == null)
685 if (drawValues && annotations[i].displayCharacter != null
686 && annotations[i].displayCharacter.length() > 1)
691 if (annotations[i].value > max)
693 max = annotations[i].value;
696 if (annotations[i].value < min)
698 min = annotations[i].value;
700 if (_linecolour == null && annotations[i].colour != null)
702 _linecolour = annotations[i].colour;
705 // ensure zero is origin for min/max ranges on only one side of zero
722 areLabelsSecondaryStructure();
724 if (!drawValues && graphType != NO_GRAPH)
726 for (int i = 0; i < annotations.length; i++)
728 if (annotations[i] != null)
730 annotations[i].displayCharacter = "";
737 * Copy constructor creates a new independent annotation row with the same
738 * associated sequenceRef
742 public AlignmentAnnotation(AlignmentAnnotation annotation)
745 this.label = new String(annotation.label);
746 if (annotation.description != null)
748 this.description = new String(annotation.description);
750 this.graphMin = annotation.graphMin;
751 this.graphMax = annotation.graphMax;
752 this.graph = annotation.graph;
753 this.graphHeight = annotation.graphHeight;
754 this.graphGroup = annotation.graphGroup;
755 this.groupRef = annotation.groupRef;
756 this.editable = annotation.editable;
757 this.autoCalculated = annotation.autoCalculated;
758 this.hasIcons = annotation.hasIcons;
759 this.hasText = annotation.hasText;
760 this.height = annotation.height;
761 this.label = annotation.label;
762 this.padGaps = annotation.padGaps;
763 this.visible = annotation.visible;
764 this.centreColLabels = annotation.centreColLabels;
765 this.scaleColLabel = annotation.scaleColLabel;
766 this.showAllColLabels = annotation.showAllColLabels;
767 this.calcId = annotation.calcId;
768 if (annotation.properties != null)
770 properties = new HashMap<>();
771 for (Map.Entry<String, String> val : annotation.properties.entrySet())
773 properties.put(val.getKey(), val.getValue());
776 if (this.hasScore = annotation.hasScore)
778 this.score = annotation.score;
780 if (annotation.threshold != null)
782 threshold = new GraphLine(annotation.threshold);
784 Annotation[] ann = annotation.annotations;
785 if (annotation.annotations != null)
787 this.annotations = new Annotation[ann.length];
788 for (int i = 0; i < ann.length; i++)
792 annotations[i] = new Annotation(ann[i]);
793 if (_linecolour != null)
795 _linecolour = annotations[i].colour;
800 if (annotation.sequenceRef != null)
802 this.sequenceRef = annotation.sequenceRef;
803 if (annotation.sequenceMapping != null)
806 sequenceMapping = new HashMap<>();
807 Iterator<Integer> pos = annotation.sequenceMapping.keySet()
809 while (pos.hasNext())
811 // could optimise this!
813 Annotation a = annotation.sequenceMapping.get(p);
820 for (int i = 0; i < ann.length; i++)
824 sequenceMapping.put(p, annotations[i]);
832 this.sequenceMapping = null;
836 // TODO: check if we need to do this: JAL-952
837 // if (this.isrna=annotation.isrna)
839 // _rnasecstr=new SequenceFeature[annotation._rnasecstr];
841 validateRangeAndDisplay(); // construct hashcodes, etc.
845 * clip the annotation to the columns given by startRes and endRes (inclusive)
846 * and prune any existing sequenceMapping to just those columns.
851 public void restrict(int startRes, int endRes)
853 if (annotations == null)
862 if (startRes >= annotations.length)
864 startRes = annotations.length - 1;
866 if (endRes >= annotations.length)
868 endRes = annotations.length - 1;
870 if (annotations == null)
874 Annotation[] temp = new Annotation[endRes - startRes + 1];
875 if (startRes < annotations.length)
877 System.arraycopy(annotations, startRes, temp, 0,
878 endRes - startRes + 1);
880 if (sequenceRef != null)
882 // Clip the mapping, if it exists.
883 int spos = sequenceRef.findPosition(startRes);
884 int epos = sequenceRef.findPosition(endRes);
885 if (sequenceMapping != null)
887 Map<Integer, Annotation> newmapping = new HashMap<>();
888 Iterator<Integer> e = sequenceMapping.keySet().iterator();
891 Integer pos = e.next();
892 if (pos.intValue() >= spos && pos.intValue() <= epos)
894 newmapping.put(pos, sequenceMapping.get(pos));
897 sequenceMapping.clear();
898 sequenceMapping = newmapping;
905 * set the annotation row to be at least length Annotations
908 * minimum number of columns required in the annotation row
909 * @return false if the annotation row is greater than length
911 public boolean padAnnotation(int length)
913 if (annotations == null)
915 return true; // annotation row is correct - null == not visible and
918 if (annotations.length < length)
920 Annotation[] na = new Annotation[length];
921 System.arraycopy(annotations, 0, na, 0, annotations.length);
925 return annotations.length > length;
932 * @return DOCUMENT ME!
935 public String toString()
937 if (annotations == null)
941 StringBuilder buffer = new StringBuilder(256);
943 for (int i = 0; i < annotations.length; i++)
945 if (annotations[i] != null)
949 buffer.append(annotations[i].value);
953 buffer.append(annotations[i].secondaryStructure);
957 buffer.append(annotations[i].displayCharacter);
963 // TODO: remove disgusting hack for 'special' treatment of consensus line.
964 if (label.indexOf("Consensus") == 0)
968 for (int i = 0; i < annotations.length; i++)
970 if (annotations[i] != null)
972 buffer.append(annotations[i].description);
979 return buffer.toString();
982 public void setThreshold(GraphLine line)
987 public GraphLine getThreshold()
993 * Attach the annotation to seqRef, starting from startRes position. If
994 * alreadyMapped is true then the indices of the annotation[] array are
995 * sequence positions rather than alignment column positions.
999 * @param alreadyMapped
1001 public void createSequenceMapping(SequenceI seqRef, int startRes,
1002 boolean alreadyMapped)
1009 sequenceRef = seqRef;
1010 if (annotations == null)
1014 sequenceMapping = new HashMap<>();
1018 for (int i = 0; i < annotations.length; i++)
1020 if (annotations[i] != null)
1024 seqPos = seqRef.findPosition(i);
1028 seqPos = i + startRes;
1031 sequenceMapping.put(Integer.valueOf(seqPos), annotations[i]);
1038 * When positional annotation and a sequence reference is present, clears and
1039 * resizes the annotations array to the current alignment width, and adds
1040 * annotation according to aligned positions of the sequenceRef given by
1043 public void adjustForAlignment()
1045 if (sequenceRef == null)
1050 if (annotations == null)
1055 int a = 0, aSize = sequenceRef.getLength();
1064 Annotation[] temp = new Annotation[aSize];
1066 if (sequenceMapping != null)
1068 for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++)
1070 index = Integer.valueOf(a);
1071 Annotation annot = sequenceMapping.get(index);
1074 position = sequenceRef.findIndex(a) - 1;
1076 temp[position] = annot;
1084 * remove any null entries in annotation row and return the number of non-null
1085 * annotation elements.
1089 public int compactAnnotationArray()
1091 int i = 0, iSize = annotations.length;
1094 if (annotations[i] == null)
1098 System.arraycopy(annotations, i + 1, annotations, i,
1108 Annotation[] ann = annotations;
1109 annotations = new Annotation[i];
1110 System.arraycopy(ann, 0, annotations, 0, i);
1116 * Associate this annotation with the aligned residues of a particular
1117 * sequence. sequenceMapping will be updated in the following way: null
1118 * sequenceI - existing mapping will be discarded but annotations left in
1119 * mapped positions. valid sequenceI not equal to current sequenceRef: mapping
1120 * is discarded and rebuilt assuming 1:1 correspondence TODO: overload with
1121 * parameter to specify correspondence between current and new sequenceRef
1125 public void setSequenceRef(SequenceI sequenceI)
1127 if (sequenceI != null)
1129 if (sequenceRef != null)
1131 boolean rIsDs = sequenceRef.getDatasetSequence() == null,
1132 tIsDs = sequenceI.getDatasetSequence() == null;
1133 if (sequenceRef != sequenceI
1135 && sequenceRef != sequenceI.getDatasetSequence())
1137 && sequenceRef.getDatasetSequence() != sequenceI)
1138 && (!rIsDs && !tIsDs
1139 && sequenceRef.getDatasetSequence() != sequenceI
1140 .getDatasetSequence())
1141 && !sequenceRef.equals(sequenceI))
1143 // if sequenceRef isn't intersecting with sequenceI
1144 // throw away old mapping and reconstruct.
1146 if (sequenceMapping != null)
1148 sequenceMapping = null;
1149 // compactAnnotationArray();
1151 createSequenceMapping(sequenceI, 1, true);
1152 adjustForAlignment();
1156 // Mapping carried over
1157 sequenceRef = sequenceI;
1162 // No mapping exists
1163 createSequenceMapping(sequenceI, 1, true);
1164 adjustForAlignment();
1169 // throw away the mapping without compacting.
1170 sequenceMapping = null;
1178 public double getScore()
1187 public void setScore(double score)
1195 * @return true if annotation has an associated score
1197 public boolean hasScore()
1199 return hasScore || !Double.isNaN(score);
1203 * Score only annotation
1206 * @param description
1209 public AlignmentAnnotation(String label, String description, double score)
1211 this(label, description, null);
1216 * copy constructor with edit based on the hidden columns marked in colSel
1218 * @param alignmentAnnotation
1221 public AlignmentAnnotation(AlignmentAnnotation alignmentAnnotation,
1222 HiddenColumns hidden)
1224 this(alignmentAnnotation);
1225 if (annotations == null)
1229 makeVisibleAnnotation(hidden);
1232 public void setPadGaps(boolean padgaps, char gapchar)
1234 this.padGaps = padgaps;
1238 for (int i = 0; i < annotations.length; i++)
1240 if (annotations[i] == null)
1242 annotations[i] = new Annotation(String.valueOf(gapchar), null,
1245 else if (annotations[i].displayCharacter == null
1246 || annotations[i].displayCharacter.equals(" "))
1248 annotations[i].displayCharacter = String.valueOf(gapchar);
1255 * format description string for display
1258 * @return Get the annotation description string optionally prefixed by
1259 * associated sequence name (if any)
1261 public String getDescription(boolean seqname)
1263 if (seqname && this.sequenceRef != null)
1265 int i = description.toLowerCase(Locale.ROOT).indexOf("<html>");
1268 // move the html tag to before the sequence reference.
1269 return "<html>" + sequenceRef.getName() + " : "
1270 + description.substring(i + 6);
1272 return sequenceRef.getName() + " : " + description;
1277 public boolean isValidStruc()
1279 return invalidrnastruc == -1;
1282 public long getInvalidStrucPos()
1284 return invalidrnastruc;
1288 * machine readable ID string indicating what generated this annotation
1290 protected String calcId = "";
1293 * properties associated with the calcId
1295 protected Map<String, String> properties = new HashMap<>();
1298 * base colour for line graphs. If null, will be set automatically by
1299 * searching the alignment annotation
1301 public java.awt.Color _linecolour;
1303 public String getCalcId()
1308 public void setCalcId(String calcId)
1310 this.calcId = calcId;
1313 public boolean isRNA()
1319 * transfer annotation to the given sequence using the given mapping from the
1320 * current positions or an existing sequence mapping
1324 * map involving sq as To or From
1326 public void liftOver(SequenceI sq, Mapping sp2sq)
1328 if (sp2sq.getMappedWidth() != sp2sq.getWidth())
1330 // TODO: employ getWord/MappedWord to transfer annotation between cDNA and
1331 // Protein reference frames
1333 "liftOver currently not implemented for transfer of annotation between different types of seqeunce");
1335 boolean mapIsTo = (sp2sq != null)
1336 ? (sp2sq.getTo() == sq
1337 || sp2sq.getTo() == sq.getDatasetSequence())
1340 // TODO build a better annotation element map and get rid of annotations[]
1341 Map<Integer, Annotation> mapForsq = new HashMap<>();
1342 if (sequenceMapping != null)
1346 for (Entry<Integer, Annotation> ie : sequenceMapping.entrySet())
1348 Integer mpos = Integer
1349 .valueOf(mapIsTo ? sp2sq.getMappedPosition(ie.getKey())
1350 : sp2sq.getPosition(ie.getKey()));
1351 if (mpos >= sq.getStart() && mpos <= sq.getEnd())
1353 mapForsq.put(mpos, ie.getValue());
1356 sequenceMapping = mapForsq;
1358 adjustForAlignment();
1368 * like liftOver but more general.
1370 * Takes an array of int pairs that will be used to update the internal
1371 * sequenceMapping and so shuffle the annotated positions
1374 * - new sequence reference for the annotation row - if null,
1375 * sequenceRef is left unchanged
1377 * array of ints containing corresponding positions
1379 * - column for current coordinate system (-1 for index+1)
1381 * - column for destination coordinate system (-1 for index+1)
1383 * - offset added to index when referencing either coordinate system
1384 * @note no checks are made as to whether from and/or to are sensible
1385 * @note caller should add the remapped annotation to newref if they have not
1388 public void remap(SequenceI newref, HashMap<Integer, int[]> mapping,
1389 int from, int to, int idxoffset)
1391 if (mapping != null)
1393 Map<Integer, Annotation> old = sequenceMapping;
1394 Map<Integer, Annotation> remap = new HashMap<>();
1396 for (int mp[] : mapping.values())
1402 Annotation ann = null;
1405 ann = sequenceMapping.get(Integer.valueOf(idxoffset + index));
1409 if (mp != null && mp.length > from)
1411 ann = sequenceMapping.get(Integer.valueOf(mp[from]));
1418 remap.put(Integer.valueOf(idxoffset + index), ann);
1422 if (to > -1 && to < mp.length)
1424 remap.put(Integer.valueOf(mp[to]), ann);
1429 sequenceMapping = remap;
1433 sequenceRef = newref;
1435 adjustForAlignment();
1439 public String getProperty(String property)
1441 if (properties == null)
1445 return properties.get(property);
1448 public void setProperty(String property, String value)
1450 if (properties == null)
1452 properties = new HashMap<>();
1454 properties.put(property, value);
1457 public boolean hasProperties()
1459 return properties != null && properties.size() > 0;
1462 public Collection<String> getProperties()
1464 if (properties == null)
1466 return Collections.emptyList();
1468 return properties.keySet();
1472 * Returns the Annotation for the given sequence position (base 1) if any,
1478 public Annotation getAnnotationForPosition(int position)
1480 return sequenceMapping == null ? null : sequenceMapping.get(position);
1485 * Set the id to "ann" followed by a counter that increments so as to be
1486 * unique for the lifetime of the JVM
1488 protected final void setAnnotationId()
1490 this.annotationId = ANNOTATION_ID_PREFIX + Long.toString(nextId());
1494 * Returns the match for the last unmatched opening RNA helix pair symbol
1495 * preceding the given column, or '(' if nothing found to match.
1500 public String getDefaultRnaHelixSymbol(int column)
1502 String result = "(";
1503 if (annotations == null)
1509 * for each preceding column, if it contains an open bracket,
1510 * count whether it is still unmatched at column, if so return its pair
1511 * (likely faster than the fancy alternative using stacks)
1513 for (int col = column - 1; col >= 0; col--)
1515 Annotation annotation = annotations[col];
1516 if (annotation == null)
1520 String displayed = annotation.displayCharacter;
1521 if (displayed == null || displayed.length() != 1)
1525 char symbol = displayed.charAt(0);
1526 if (!Rna.isOpeningParenthesis(symbol))
1532 * found an opening bracket symbol
1533 * count (closing-opening) symbols of this type that follow it,
1534 * up to and excluding the target column; if the count is less
1535 * than 1, the opening bracket is unmatched, so return its match
1537 String closer = String
1538 .valueOf(Rna.getMatchingClosingParenthesis(symbol));
1539 String opener = String.valueOf(symbol);
1541 for (int j = col + 1; j < column; j++)
1543 if (annotations[j] != null)
1545 String s = annotations[j].displayCharacter;
1546 if (closer.equals(s))
1550 else if (opener.equals(s))
1564 protected static synchronized long nextId()
1571 * @return true for rows that have a range of values in their annotation set
1573 public boolean isQuantitative()
1575 return graphMin < graphMax;
1579 * delete any columns in alignmentAnnotation that are hidden (including
1580 * sequence associated annotation).
1582 * @param hiddenColumns
1583 * the set of hidden columns
1585 public void makeVisibleAnnotation(HiddenColumns hiddenColumns)
1587 if (annotations != null)
1589 makeVisibleAnnotation(0, annotations.length, hiddenColumns);
1594 * delete any columns in alignmentAnnotation that are hidden (including
1595 * sequence associated annotation).
1598 * remove any annotation to the right of this column
1600 * remove any annotation to the left of this column
1601 * @param hiddenColumns
1602 * the set of hidden columns
1604 public void makeVisibleAnnotation(int start, int end,
1605 HiddenColumns hiddenColumns)
1607 if (annotations != null)
1609 if (hiddenColumns.hasHiddenColumns())
1611 removeHiddenAnnotation(start, end, hiddenColumns);
1615 restrict(start, end);
1621 * The actual implementation of deleting hidden annotation columns
1624 * remove any annotation to the right of this column
1626 * remove any annotation to the left of this column
1627 * @param hiddenColumns
1628 * the set of hidden columns
1630 private void removeHiddenAnnotation(int start, int end,
1631 HiddenColumns hiddenColumns)
1633 // mangle the alignmentAnnotation annotation array
1634 ArrayList<Annotation[]> annels = new ArrayList<>();
1635 Annotation[] els = null;
1639 Iterator<int[]> blocks = hiddenColumns.getVisContigsIterator(start,
1643 int annotationLength;
1644 while (blocks.hasNext())
1646 int[] block = blocks.next();
1647 annotationLength = block[1] - block[0] + 1;
1649 if (blocks.hasNext())
1651 // copy just the visible segment of the annotation row
1652 copylength = annotationLength;
1656 if (annotationLength + block[0] <= annotations.length)
1658 // copy just the visible segment of the annotation row
1659 copylength = annotationLength;
1663 // copy to the end of the annotation row
1664 copylength = annotations.length - block[0];
1668 els = new Annotation[annotationLength];
1670 System.arraycopy(annotations, block[0], els, 0, copylength);
1671 w += annotationLength;
1676 annotations = new Annotation[w];
1679 for (Annotation[] chnk : annels)
1681 System.arraycopy(chnk, 0, annotations, w, chnk.length);
1687 public static Iterable<AlignmentAnnotation> findAnnotations(
1688 Iterable<AlignmentAnnotation> list, SequenceI seq, String calcId,
1692 ArrayList<AlignmentAnnotation> aa = new ArrayList<>();
1693 for (AlignmentAnnotation ann : list)
1695 if ((calcId == null || (ann.getCalcId() != null
1696 && ann.getCalcId().equals(calcId)))
1697 && (seq == null || (ann.sequenceRef != null
1698 && ann.sequenceRef == seq))
1700 || (ann.label != null && ann.label.equals(label))))
1709 * Answer true if any annotation matches the calcId passed in (if not null).
1712 * annotation to search
1716 public static boolean hasAnnotation(List<AlignmentAnnotation> list,
1720 if (calcId != null && !"".equals(calcId))
1722 for (AlignmentAnnotation a : list)
1724 if (a.getCalcId() == calcId)
1733 public static Iterable<AlignmentAnnotation> findAnnotation(
1734 List<AlignmentAnnotation> list, String calcId)
1737 List<AlignmentAnnotation> aa = new ArrayList<>();
1742 for (AlignmentAnnotation a : list)
1745 if (a.getCalcId() == calcId || (a.getCalcId() != null
1746 && calcId != null && a.getCalcId().equals(calcId)))
1755 * convenience method to check for the 'CONTACT_MAP_NOGROUPS' property for this alignment annotation row
1756 * @return true if no CONTACT_MAP_NOGROUPS property is found, or it is set to ""
1758 public boolean isShowGroupsForContactMatrix()
1760 return getProperty(AlignmentAnnotation.CONTACT_MAP_NOGROUPS)==null || "".equals(getProperty(AlignmentAnnotation.CONTACT_MAP_NOGROUPS));
1763 * set the 'CONTACT_MAP_NOGROUPS' property for this alignment annotation row
1764 * @see isShowGroupsForContactMatrix
1766 public void setShowGroupsForContactMatrix(boolean showGroups)
1768 setProperty(AlignmentAnnotation.CONTACT_MAP_NOGROUPS, showGroups ? "" : "nogroups");