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.Collection;
29 import java.util.Collections;
30 import java.util.HashMap;
31 import java.util.Iterator;
32 import java.util.List;
34 import java.util.Map.Entry;
42 public class AlignmentAnnotation
44 private static final String ANNOTATION_ID_PREFIX = "ann";
47 * Identifers for different types of profile data
49 public static final int SEQUENCE_PROFILE = 0;
51 public static final int STRUCTURE_PROFILE = 1;
53 public static final int CDNA_PROFILE = 2;
55 private static long counter = 0;
58 * If true, this annotations is calculated every edit, eg consensus, quality
59 * or conservation graphs
61 public boolean autoCalculated = false;
64 * unique ID for this annotation, used to match up the same annotation row
65 * shown in multiple views and alignments
67 public String annotationId;
70 * the sequence this annotation is associated with (or null)
72 public SequenceI sequenceRef;
74 /** label shown in dropdown menus and in the annotation label area */
77 /** longer description text shown as a tooltip */
78 public String description;
80 /** Array of annotations placed in the current coordinate system */
81 public Annotation[] annotations;
83 public List<SimpleBP> bps = null;
86 * RNA secondary structure contact positions
88 public SequenceFeature[] _rnasecstr = null;
91 * position of annotation resulting in invalid WUSS parsing or -1. -2 means
92 * there was no RNA structure in this annotation
94 private long invalidrnastruc = -2;
97 * Updates the _rnasecstr field Determines the positions that base pair and
98 * the positions of helices based on secondary structure from a Stockholm file
100 * @param rnaAnnotation
102 private void _updateRnaSecStr(CharSequence rnaAnnotation)
106 _rnasecstr = Rna.getHelixMap(rnaAnnotation);
107 invalidrnastruc = -1;
108 } catch (WUSSParseException px)
110 // DEBUG System.out.println(px);
111 invalidrnastruc = px.getProblemPos();
113 if (invalidrnastruc > -1)
118 if (_rnasecstr != null && _rnasecstr.length > 0)
120 // show all the RNA secondary structure annotation symbols.
122 showAllColLabels = true;
123 scaleColLabel = true;
126 // System.out.println("featuregroup " + _rnasecstr[0].getFeatureGroup());
130 private void _markRnaHelices()
133 // Figure out number of helices
134 // Length of rnasecstr is the number of pairs of positions that base pair
135 // with each other in the secondary structure
136 for (int x = 0; x < _rnasecstr.length; x++)
140 * System.out.println(this.annotation._rnasecstr[x] + " Begin" +
141 * this.annotation._rnasecstr[x].getBegin());
143 // System.out.println(this.annotation._rnasecstr[x].getFeatureGroup());
147 val = Integer.valueOf(_rnasecstr[x].getFeatureGroup());
152 } catch (NumberFormatException q)
157 annotations[_rnasecstr[x].getBegin()].value = val;
158 annotations[_rnasecstr[x].getEnd()].value = val;
160 // annotations[_rnasecstr[x].getBegin()].displayCharacter = "" + val;
161 // annotations[_rnasecstr[x].getEnd()].displayCharacter = "" + val;
167 * map of positions in the associated annotation
169 private Map<Integer, Annotation> sequenceMapping;
172 * lower range for quantitative data
174 public float graphMin;
177 * Upper range for quantitative data
179 public float graphMax;
182 * Score associated with label and description.
184 public double score = Double.NaN;
187 * flag indicating if annotation has a score.
189 public boolean hasScore = false;
191 public GraphLine threshold;
193 // Graphical hints and tips
195 /** Can this row be edited by the user ? */
196 public boolean editable = false;
198 /** Indicates if annotation has a graphical symbol track */
199 public boolean hasIcons; //
201 /** Indicates if annotation has a text character label */
202 public boolean hasText;
204 /** is the row visible */
205 public boolean visible = true;
207 public int graphGroup = -1;
209 /** Displayed height of row in pixels */
210 public int height = 0;
212 public int graph = 0;
214 public int graphHeight = 40;
216 public boolean padGaps = false;
218 public static final int NO_GRAPH = 0;
220 public static final int BAR_GRAPH = 1;
222 public static final int LINE_GRAPH = 2;
224 public boolean belowAlignment = true;
226 public SequenceGroup groupRef = null;
229 * display every column label, even if there is a row of identical labels
231 public boolean showAllColLabels = false;
234 * scale the column label to fit within the alignment column.
236 public boolean scaleColLabel = false;
239 * centre the column labels relative to the alignment column
241 public boolean centreColLabels = false;
243 private boolean isrna;
245 public static int getGraphValueFromString(String string)
247 if (string.equalsIgnoreCase("BAR_GRAPH"))
251 else if (string.equalsIgnoreCase("LINE_GRAPH"))
262 * Creates a new AlignmentAnnotation object.
265 * short label shown under sequence labels
267 * text displayed on mouseover
269 * set of positional annotation elements
271 public AlignmentAnnotation(String label, String description,
272 Annotation[] annotations)
278 this.description = description;
279 this.annotations = annotations;
281 validateRangeAndDisplay();
285 * Checks if annotation labels represent secondary structures
288 void areLabelsSecondaryStructure()
290 boolean nonSSLabel = false;
292 StringBuffer rnastring = new StringBuffer();
295 for (int i = 0; i < annotations.length; i++)
297 if (annotations[i] == null)
301 if (annotations[i].secondaryStructure == 'H'
302 || annotations[i].secondaryStructure == 'E')
307 // Check for RNA secondary structure
309 // System.out.println(annotations[i].secondaryStructure);
310 // TODO: 2.8.2 should this ss symbol validation check be a function in
311 // RNA/ResidueProperties ?
312 if (annotations[i].secondaryStructure == '('
313 || annotations[i].secondaryStructure == '['
314 || annotations[i].secondaryStructure == '<'
315 || annotations[i].secondaryStructure == '{'
316 || annotations[i].secondaryStructure == 'A'
317 || annotations[i].secondaryStructure == 'B'
318 || annotations[i].secondaryStructure == 'C'
319 || annotations[i].secondaryStructure == 'D'
320 || annotations[i].secondaryStructure == 'E'
321 || annotations[i].secondaryStructure == 'F'
322 || annotations[i].secondaryStructure == 'G'
323 || annotations[i].secondaryStructure == 'H'
324 || annotations[i].secondaryStructure == 'I'
325 || annotations[i].secondaryStructure == 'J'
326 || annotations[i].secondaryStructure == 'K'
327 || annotations[i].secondaryStructure == 'L'
328 || annotations[i].secondaryStructure == 'M'
329 || annotations[i].secondaryStructure == 'N'
330 || annotations[i].secondaryStructure == 'O'
331 || annotations[i].secondaryStructure == 'P'
332 || annotations[i].secondaryStructure == 'Q'
333 || annotations[i].secondaryStructure == 'R'
334 || annotations[i].secondaryStructure == 'S'
335 || annotations[i].secondaryStructure == 'T'
336 || annotations[i].secondaryStructure == 'U'
337 || annotations[i].secondaryStructure == 'V'
338 || annotations[i].secondaryStructure == 'W'
339 || annotations[i].secondaryStructure == 'X'
340 || annotations[i].secondaryStructure == 'Y'
341 || annotations[i].secondaryStructure == 'Z')
348 // System.out.println("displaychar " + annotations[i].displayCharacter);
350 if (annotations[i].displayCharacter == null
351 || annotations[i].displayCharacter.length() == 0)
353 rnastring.append('.');
356 if (annotations[i].displayCharacter.length() == 1)
358 firstChar = annotations[i].displayCharacter.charAt(0);
359 // check to see if it looks like a sequence or is secondary structure
361 if (annotations[i].secondaryStructure != ' ' && !hasIcons &&
362 // Uncomment to only catch case where
363 // displayCharacter==secondary
365 // to correctly redisplay SS annotation imported from Stockholm,
366 // exported to JalviewXML and read back in again.
368 // annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure
369 firstChar != ' ' && firstChar != '$' && firstChar != 0xCE
370 && firstChar != '(' && firstChar != '[' && firstChar != '>'
371 && firstChar != '{' && firstChar != 'A' && firstChar != 'B'
372 && firstChar != 'C' && firstChar != 'D' && firstChar != 'E'
373 && firstChar != 'F' && firstChar != 'G' && firstChar != 'H'
374 && firstChar != 'I' && firstChar != 'J' && firstChar != 'K'
375 && firstChar != 'L' && firstChar != 'M' && firstChar != 'N'
376 && firstChar != 'O' && firstChar != 'P' && firstChar != 'Q'
377 && firstChar != 'R' && firstChar != 'S' && firstChar != 'T'
378 && firstChar != 'U' && firstChar != 'V' && firstChar != 'W'
379 && firstChar != 'X' && firstChar != 'Y' && firstChar != 'Z'
381 && firstChar < jalview.schemes.ResidueProperties.aaIndex.length)
383 if (jalview.schemes.ResidueProperties.aaIndex[firstChar] < 23) // TODO:
396 rnastring.append(annotations[i].displayCharacter.charAt(1));
399 if (annotations[i].displayCharacter.length() > 0)
408 for (int j = 0; j < annotations.length; j++)
410 if (annotations[j] != null
411 && annotations[j].secondaryStructure != ' ')
413 annotations[j].displayCharacter = String
414 .valueOf(annotations[j].secondaryStructure);
415 annotations[j].secondaryStructure = ' ';
424 _updateRnaSecStr(new AnnotCharSequence());
430 * flyweight access to positions in the alignment annotation row for RNA
436 private class AnnotCharSequence implements CharSequence
442 public AnnotCharSequence()
444 this(0, annotations.length);
447 AnnotCharSequence(int start, int end)
454 public CharSequence subSequence(int start, int end)
456 return new AnnotCharSequence(offset + start, offset + end);
466 public char charAt(int index)
468 return ((index + offset < 0) || (index + offset) >= max
469 || annotations[index + offset] == null
470 || (annotations[index + offset].secondaryStructure <= ' ')
472 : annotations[index + offset].displayCharacter == null
474 + offset].displayCharacter
477 + offset].secondaryStructure
479 + offset].displayCharacter
484 public String toString()
486 char[] string = new char[max - offset];
487 int mx = annotations.length;
489 for (int i = offset; i < mx; i++)
491 string[i] = (annotations[i] == null
492 || (annotations[i].secondaryStructure <= 32))
494 : (annotations[i].displayCharacter == null
495 || annotations[i].displayCharacter
497 ? annotations[i].secondaryStructure
498 : annotations[i].displayCharacter
501 return new String(string);
505 private long _lastrnaannot = -1;
507 public String getRNAStruc()
511 String rnastruc = new AnnotCharSequence().toString();
512 if (_lastrnaannot != rnastruc.hashCode())
514 // ensure rna structure contacts are up to date
515 _lastrnaannot = rnastruc.hashCode();
516 _updateRnaSecStr(rnastruc);
524 * Creates a new AlignmentAnnotation object.
539 public AlignmentAnnotation(String label, String description,
540 Annotation[] annotations, float min, float max, int graphType)
543 // graphs are not editable
544 editable = graphType == 0;
547 this.description = description;
548 this.annotations = annotations;
552 validateRangeAndDisplay();
556 * checks graphMin and graphMax, secondary structure symbols, sets graphType
557 * appropriately, sets null labels to the empty string if appropriate.
559 public void validateRangeAndDisplay()
562 if (annotations == null)
564 visible = false; // try to prevent renderer from displaying.
565 invalidrnastruc = -1;
566 return; // this is a non-annotation row annotation - ie a sequence score.
569 int graphType = graph;
570 float min = graphMin;
571 float max = graphMax;
572 boolean drawValues = true;
577 for (int i = 0; i < annotations.length; i++)
579 if (annotations[i] == null)
584 if (drawValues && annotations[i].displayCharacter != null
585 && annotations[i].displayCharacter.length() > 1)
590 if (annotations[i].value > max)
592 max = annotations[i].value;
595 if (annotations[i].value < min)
597 min = annotations[i].value;
599 if (_linecolour == null && annotations[i].colour != null)
601 _linecolour = annotations[i].colour;
604 // ensure zero is origin for min/max ranges on only one side of zero
621 areLabelsSecondaryStructure();
623 if (!drawValues && graphType != NO_GRAPH)
625 for (int i = 0; i < annotations.length; i++)
627 if (annotations[i] != null)
629 annotations[i].displayCharacter = "";
636 * Copy constructor creates a new independent annotation row with the same
637 * associated sequenceRef
641 public AlignmentAnnotation(AlignmentAnnotation annotation)
644 this.label = new String(annotation.label);
645 if (annotation.description != null)
647 this.description = new String(annotation.description);
649 this.graphMin = annotation.graphMin;
650 this.graphMax = annotation.graphMax;
651 this.graph = annotation.graph;
652 this.graphHeight = annotation.graphHeight;
653 this.graphGroup = annotation.graphGroup;
654 this.groupRef = annotation.groupRef;
655 this.editable = annotation.editable;
656 this.autoCalculated = annotation.autoCalculated;
657 this.hasIcons = annotation.hasIcons;
658 this.hasText = annotation.hasText;
659 this.height = annotation.height;
660 this.label = annotation.label;
661 this.padGaps = annotation.padGaps;
662 this.visible = annotation.visible;
663 this.centreColLabels = annotation.centreColLabels;
664 this.scaleColLabel = annotation.scaleColLabel;
665 this.showAllColLabels = annotation.showAllColLabels;
666 this.calcId = annotation.calcId;
667 if (annotation.properties != null)
669 properties = new HashMap<String, String>();
670 for (Map.Entry<String, String> val : annotation.properties.entrySet())
672 properties.put(val.getKey(), val.getValue());
675 if (this.hasScore = annotation.hasScore)
677 this.score = annotation.score;
679 if (annotation.threshold != null)
681 threshold = new GraphLine(annotation.threshold);
683 Annotation[] ann = annotation.annotations;
684 if (annotation.annotations != null)
686 this.annotations = new Annotation[ann.length];
687 for (int i = 0; i < ann.length; i++)
691 annotations[i] = new Annotation(ann[i]);
692 if (_linecolour != null)
694 _linecolour = annotations[i].colour;
699 if (annotation.sequenceRef != null)
701 this.sequenceRef = annotation.sequenceRef;
702 if (annotation.sequenceMapping != null)
705 sequenceMapping = new HashMap<Integer, Annotation>();
706 Iterator<Integer> pos = annotation.sequenceMapping.keySet()
708 while (pos.hasNext())
710 // could optimise this!
712 Annotation a = annotation.sequenceMapping.get(p);
719 for (int i = 0; i < ann.length; i++)
723 sequenceMapping.put(p, annotations[i]);
731 this.sequenceMapping = null;
734 // TODO: check if we need to do this: JAL-952
735 // if (this.isrna=annotation.isrna)
737 // _rnasecstr=new SequenceFeature[annotation._rnasecstr];
739 validateRangeAndDisplay(); // construct hashcodes, etc.
743 * clip the annotation to the columns given by startRes and endRes (inclusive)
744 * and prune any existing sequenceMapping to just those columns.
749 public void restrict(int startRes, int endRes)
751 if (annotations == null)
760 if (startRes >= annotations.length)
762 startRes = annotations.length - 1;
764 if (endRes >= annotations.length)
766 endRes = annotations.length - 1;
768 if (annotations == null)
772 Annotation[] temp = new Annotation[endRes - startRes + 1];
773 if (startRes < annotations.length)
775 System.arraycopy(annotations, startRes, temp, 0,
776 endRes - startRes + 1);
778 if (sequenceRef != null)
780 // Clip the mapping, if it exists.
781 int spos = sequenceRef.findPosition(startRes);
782 int epos = sequenceRef.findPosition(endRes);
783 if (sequenceMapping != null)
785 Map<Integer, Annotation> newmapping = new HashMap<Integer, Annotation>();
786 Iterator<Integer> e = sequenceMapping.keySet().iterator();
789 Integer pos = e.next();
790 if (pos.intValue() >= spos && pos.intValue() <= epos)
792 newmapping.put(pos, sequenceMapping.get(pos));
795 sequenceMapping.clear();
796 sequenceMapping = newmapping;
803 * set the annotation row to be at least length Annotations
806 * minimum number of columns required in the annotation row
807 * @return false if the annotation row is greater than length
809 public boolean padAnnotation(int length)
811 if (annotations == null)
813 return true; // annotation row is correct - null == not visible and
816 if (annotations.length < length)
818 Annotation[] na = new Annotation[length];
819 System.arraycopy(annotations, 0, na, 0, annotations.length);
823 return annotations.length > length;
830 * @return DOCUMENT ME!
833 public String toString()
835 if (annotations == null)
839 StringBuilder buffer = new StringBuilder(256);
841 for (int i = 0; i < annotations.length; i++)
843 if (annotations[i] != null)
847 buffer.append(annotations[i].value);
851 buffer.append(annotations[i].secondaryStructure);
855 buffer.append(annotations[i].displayCharacter);
861 // TODO: remove disgusting hack for 'special' treatment of consensus line.
862 if (label.indexOf("Consensus") == 0)
866 for (int i = 0; i < annotations.length; i++)
868 if (annotations[i] != null)
870 buffer.append(annotations[i].description);
877 return buffer.toString();
880 public void setThreshold(GraphLine line)
885 public GraphLine getThreshold()
891 * Attach the annotation to seqRef, starting from startRes position. If
892 * alreadyMapped is true then the indices of the annotation[] array are
893 * sequence positions rather than alignment column positions.
897 * @param alreadyMapped
899 public void createSequenceMapping(SequenceI seqRef, int startRes,
900 boolean alreadyMapped)
907 sequenceRef = seqRef;
908 if (annotations == null)
912 sequenceMapping = new HashMap<Integer, Annotation>();
916 for (int i = 0; i < annotations.length; i++)
918 if (annotations[i] != null)
922 seqPos = seqRef.findPosition(i);
926 seqPos = i + startRes;
929 sequenceMapping.put(new Integer(seqPos), annotations[i]);
936 * When positional annotation and a sequence reference is present, clears and
937 * resizes the annotations array to the current alignment width, and adds
938 * annotation according to aligned positions of the sequenceRef given by
941 public void adjustForAlignment()
943 if (sequenceRef == null)
948 if (annotations == null)
953 int a = 0, aSize = sequenceRef.getLength();
962 Annotation[] temp = new Annotation[aSize];
964 if (sequenceMapping != null)
966 for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++)
968 index = new Integer(a);
969 Annotation annot = sequenceMapping.get(index);
972 position = sequenceRef.findIndex(a) - 1;
974 temp[position] = annot;
982 * remove any null entries in annotation row and return the number of non-null
983 * annotation elements.
987 public int compactAnnotationArray()
989 int i = 0, iSize = annotations.length;
992 if (annotations[i] == null)
996 System.arraycopy(annotations, i + 1, annotations, i,
1006 Annotation[] ann = annotations;
1007 annotations = new Annotation[i];
1008 System.arraycopy(ann, 0, annotations, 0, i);
1014 * Associate this annotation with the aligned residues of a particular
1015 * sequence. sequenceMapping will be updated in the following way: null
1016 * sequenceI - existing mapping will be discarded but annotations left in
1017 * mapped positions. valid sequenceI not equal to current sequenceRef: mapping
1018 * is discarded and rebuilt assuming 1:1 correspondence TODO: overload with
1019 * parameter to specify correspondence between current and new sequenceRef
1023 public void setSequenceRef(SequenceI sequenceI)
1025 if (sequenceI != null)
1027 if (sequenceRef != null)
1029 boolean rIsDs = sequenceRef.getDatasetSequence() == null,
1030 tIsDs = sequenceI.getDatasetSequence() == null;
1031 if (sequenceRef != sequenceI
1033 && sequenceRef != sequenceI.getDatasetSequence())
1035 && sequenceRef.getDatasetSequence() != sequenceI)
1036 && (!rIsDs && !tIsDs
1037 && sequenceRef.getDatasetSequence() != sequenceI
1038 .getDatasetSequence())
1039 && !sequenceRef.equals(sequenceI))
1041 // if sequenceRef isn't intersecting with sequenceI
1042 // throw away old mapping and reconstruct.
1044 if (sequenceMapping != null)
1046 sequenceMapping = null;
1047 // compactAnnotationArray();
1049 createSequenceMapping(sequenceI, 1, true);
1050 adjustForAlignment();
1054 // Mapping carried over
1055 sequenceRef = sequenceI;
1060 // No mapping exists
1061 createSequenceMapping(sequenceI, 1, true);
1062 adjustForAlignment();
1067 // throw away the mapping without compacting.
1068 sequenceMapping = null;
1076 public double getScore()
1085 public void setScore(double score)
1093 * @return true if annotation has an associated score
1095 public boolean hasScore()
1097 return hasScore || !Double.isNaN(score);
1101 * Score only annotation
1104 * @param description
1107 public AlignmentAnnotation(String label, String description, double score)
1109 this(label, description, null);
1114 * copy constructor with edit based on the hidden columns marked in colSel
1116 * @param alignmentAnnotation
1119 public AlignmentAnnotation(AlignmentAnnotation alignmentAnnotation,
1120 HiddenColumns hidden)
1122 this(alignmentAnnotation);
1123 if (annotations == null)
1127 hidden.makeVisibleAnnotation(this);
1130 public void setPadGaps(boolean padgaps, char gapchar)
1132 this.padGaps = padgaps;
1136 for (int i = 0; i < annotations.length; i++)
1138 if (annotations[i] == null)
1140 annotations[i] = new Annotation(String.valueOf(gapchar), null,
1143 else if (annotations[i].displayCharacter == null
1144 || annotations[i].displayCharacter.equals(" "))
1146 annotations[i].displayCharacter = String.valueOf(gapchar);
1153 * format description string for display
1156 * @return Get the annotation description string optionally prefixed by
1157 * associated sequence name (if any)
1159 public String getDescription(boolean seqname)
1161 if (seqname && this.sequenceRef != null)
1163 int i = description.toLowerCase().indexOf("<html>");
1166 // move the html tag to before the sequence reference.
1167 return "<html>" + sequenceRef.getName() + " : "
1168 + description.substring(i + 6);
1170 return sequenceRef.getName() + " : " + description;
1175 public boolean isValidStruc()
1177 return invalidrnastruc == -1;
1180 public long getInvalidStrucPos()
1182 return invalidrnastruc;
1186 * machine readable ID string indicating what generated this annotation
1188 protected String calcId = "";
1191 * properties associated with the calcId
1193 protected Map<String, String> properties = new HashMap<String, String>();
1196 * base colour for line graphs. If null, will be set automatically by
1197 * searching the alignment annotation
1199 public java.awt.Color _linecolour;
1201 public String getCalcId()
1206 public void setCalcId(String calcId)
1208 this.calcId = calcId;
1211 public boolean isRNA()
1217 * transfer annotation to the given sequence using the given mapping from the
1218 * current positions or an existing sequence mapping
1222 * map involving sq as To or From
1224 public void liftOver(SequenceI sq, Mapping sp2sq)
1226 if (sp2sq.getMappedWidth() != sp2sq.getWidth())
1228 // TODO: employ getWord/MappedWord to transfer annotation between cDNA and
1229 // Protein reference frames
1231 "liftOver currently not implemented for transfer of annotation between different types of seqeunce");
1233 boolean mapIsTo = (sp2sq != null)
1234 ? (sp2sq.getTo() == sq
1235 || sp2sq.getTo() == sq.getDatasetSequence())
1238 // TODO build a better annotation element map and get rid of annotations[]
1239 Map<Integer, Annotation> mapForsq = new HashMap<Integer, Annotation>();
1240 if (sequenceMapping != null)
1244 for (Entry<Integer, Annotation> ie : sequenceMapping.entrySet())
1246 Integer mpos = Integer
1247 .valueOf(mapIsTo ? sp2sq.getMappedPosition(ie.getKey())
1248 : sp2sq.getPosition(ie.getKey()));
1249 if (mpos >= sq.getStart() && mpos <= sq.getEnd())
1251 mapForsq.put(mpos, ie.getValue());
1254 sequenceMapping = mapForsq;
1256 adjustForAlignment();
1266 * like liftOver but more general.
1268 * Takes an array of int pairs that will be used to update the internal
1269 * sequenceMapping and so shuffle the annotated positions
1272 * - new sequence reference for the annotation row - if null,
1273 * sequenceRef is left unchanged
1275 * array of ints containing corresponding positions
1277 * - column for current coordinate system (-1 for index+1)
1279 * - column for destination coordinate system (-1 for index+1)
1281 * - offset added to index when referencing either coordinate system
1282 * @note no checks are made as to whether from and/or to are sensible
1283 * @note caller should add the remapped annotation to newref if they have not
1286 public void remap(SequenceI newref, HashMap<Integer, int[]> mapping,
1287 int from, int to, int idxoffset)
1289 if (mapping != null)
1291 Map<Integer, Annotation> old = sequenceMapping;
1292 Map<Integer, Annotation> remap = new HashMap<Integer, Annotation>();
1294 for (int mp[] : mapping.values())
1300 Annotation ann = null;
1303 ann = sequenceMapping.get(Integer.valueOf(idxoffset + index));
1307 if (mp != null && mp.length > from)
1309 ann = sequenceMapping.get(Integer.valueOf(mp[from]));
1316 remap.put(Integer.valueOf(idxoffset + index), ann);
1320 if (to > -1 && to < mp.length)
1322 remap.put(Integer.valueOf(mp[to]), ann);
1327 sequenceMapping = remap;
1331 sequenceRef = newref;
1333 adjustForAlignment();
1337 public String getProperty(String property)
1339 if (properties == null)
1343 return properties.get(property);
1346 public void setProperty(String property, String value)
1348 if (properties == null)
1350 properties = new HashMap<String, String>();
1352 properties.put(property, value);
1355 public boolean hasProperties()
1357 return properties != null && properties.size() > 0;
1360 public Collection<String> getProperties()
1362 if (properties == null)
1364 return Collections.emptyList();
1366 return properties.keySet();
1370 * Returns the Annotation for the given sequence position (base 1) if any,
1376 public Annotation getAnnotationForPosition(int position)
1378 return sequenceMapping == null ? null : sequenceMapping.get(position);
1383 * Set the id to "ann" followed by a counter that increments so as to be
1384 * unique for the lifetime of the JVM
1386 protected final void setAnnotationId()
1388 this.annotationId = ANNOTATION_ID_PREFIX + Long.toString(nextId());
1392 * Returns the match for the last unmatched opening RNA helix pair symbol
1393 * preceding the given column, or '(' if nothing found to match.
1398 public String getDefaultRnaHelixSymbol(int column)
1400 String result = "(";
1401 if (annotations == null)
1407 * for each preceding column, if it contains an open bracket,
1408 * count whether it is still unmatched at column, if so return its pair
1409 * (likely faster than the fancy alternative using stacks)
1411 for (int col = column - 1; col >= 0; col--)
1413 Annotation annotation = annotations[col];
1414 if (annotation == null)
1418 String displayed = annotation.displayCharacter;
1419 if (displayed == null || displayed.length() != 1)
1423 char symbol = displayed.charAt(0);
1424 if (!Rna.isOpeningParenthesis(symbol))
1430 * found an opening bracket symbol
1431 * count (closing-opening) symbols of this type that follow it,
1432 * up to and excluding the target column; if the count is less
1433 * than 1, the opening bracket is unmatched, so return its match
1435 String closer = String
1436 .valueOf(Rna.getMatchingClosingParenthesis(symbol));
1437 String opener = String.valueOf(symbol);
1439 for (int j = col + 1; j < column; j++)
1441 if (annotations[j] != null)
1443 String s = annotations[j].displayCharacter;
1444 if (closer.equals(s))
1448 else if (opener.equals(s))
1462 protected static synchronized long nextId()
1469 * @return true for rows that have a range of values in their annotation set
1471 public boolean isQuantitative()
1473 return graphMin < graphMax;
1476 public static Iterable<AlignmentAnnotation> findAnnotations(
1477 Iterable<AlignmentAnnotation> list, SequenceI seq, String calcId,
1481 ArrayList<AlignmentAnnotation> aa = new ArrayList<>();
1482 for (AlignmentAnnotation ann : list)
1484 if ((calcId == null || (ann.getCalcId() != null
1485 && ann.getCalcId().equals(calcId)))
1486 && (seq == null || (ann.sequenceRef != null
1487 && ann.sequenceRef == seq))
1489 || (ann.label != null && ann.label.equals(label))))
1498 * Answer true if any annotation matches the calcId passed in (if not null).
1501 * annotation to search
1505 public static boolean hasAnnotation(List<AlignmentAnnotation> list,
1509 if (calcId != null && !"".equals(calcId))
1511 for (AlignmentAnnotation a : list)
1513 if (a.getCalcId() == calcId)
1522 public static Iterable<AlignmentAnnotation> findAnnotation(
1523 List<AlignmentAnnotation> list, String calcId)
1526 List<AlignmentAnnotation> aa = new ArrayList<>();
1531 for (AlignmentAnnotation a : list)
1534 if (a.getCalcId() == calcId || (a.getCalcId() != null
1535 && calcId != null && a.getCalcId().equals(calcId)))