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.Collection;
28 import java.util.Collections;
29 import java.util.HashMap;
30 import java.util.Iterator;
31 import java.util.List;
33 import java.util.Map.Entry;
41 public class AlignmentAnnotation
43 private static final String ANNOTATION_ID_PREFIX = "ann";
46 * Identifers for different types of profile data
48 public static final int SEQUENCE_PROFILE = 0;
50 public static final int STRUCTURE_PROFILE = 1;
52 public static final int CDNA_PROFILE = 2;
54 private static long counter = 0;
57 * If true, this annotations is calculated every edit, eg consensus, quality
58 * or conservation graphs
60 public boolean autoCalculated = false;
63 * unique ID for this annotation, used to match up the same annotation row
64 * shown in multiple views and alignments
66 public String annotationId;
69 * the sequence this annotation is associated with (or null)
71 public SequenceI sequenceRef;
73 /** label shown in dropdown menus and in the annotation label area */
76 /** longer description text shown as a tooltip */
77 public String description;
79 /** Array of annotations placed in the current coordinate system */
80 public Annotation[] annotations;
82 public List<SimpleBP> bps = null;
85 * RNA secondary structure contact positions
87 public SequenceFeature[] _rnasecstr = null;
90 * position of annotation resulting in invalid WUSS parsing or -1. -2 means
91 * there was no RNA structure in this annotation
93 private long invalidrnastruc = -2;
96 * Updates the _rnasecstr field Determines the positions that base pair and
97 * the positions of helices based on secondary structure from a Stockholm file
101 private void _updateRnaSecStr(CharSequence RNAannot)
105 bps = Rna.getModeleBP(RNAannot);
106 _rnasecstr = Rna.getBasePairs(bps);
107 invalidrnastruc = -1;
108 } catch (WUSSParseException px)
110 // DEBUG System.out.println(px);
111 invalidrnastruc = px.getProblemPos();
113 if (invalidrnastruc > -1)
117 Rna.HelixMap(_rnasecstr);
118 // setRNAStruc(RNAannot);
120 if (_rnasecstr != null && _rnasecstr.length > 0)
122 // show all the RNA secondary structure annotation symbols.
124 showAllColLabels = true;
125 scaleColLabel = true;
128 // System.out.println("featuregroup " + _rnasecstr[0].getFeatureGroup());
132 private void _markRnaHelices()
135 // Figure out number of helices
136 // Length of rnasecstr is the number of pairs of positions that base pair
137 // with each other in the secondary structure
138 for (int x = 0; x < _rnasecstr.length; x++)
142 * System.out.println(this.annotation._rnasecstr[x] + " Begin" +
143 * this.annotation._rnasecstr[x].getBegin());
145 // System.out.println(this.annotation._rnasecstr[x].getFeatureGroup());
149 val = Integer.valueOf(_rnasecstr[x].getFeatureGroup());
154 } catch (NumberFormatException q)
159 annotations[_rnasecstr[x].getBegin()].value = val;
160 annotations[_rnasecstr[x].getEnd()].value = val;
162 // annotations[_rnasecstr[x].getBegin()].displayCharacter = "" + val;
163 // annotations[_rnasecstr[x].getEnd()].displayCharacter = "" + val;
169 * map of positions in the associated annotation
171 private Map<Integer, Annotation> sequenceMapping;
174 public float graphMin;
177 public float graphMax;
180 * Score associated with label and description.
182 public double score = Double.NaN;
185 * flag indicating if annotation has a score.
187 public boolean hasScore = false;
189 public GraphLine threshold;
191 // Graphical hints and tips
193 /** Can this row be edited by the user ? */
194 public boolean editable = false;
196 /** Indicates if annotation has a graphical symbol track */
197 public boolean hasIcons; //
199 /** Indicates if annotation has a text character label */
200 public boolean hasText;
202 /** is the row visible */
203 public boolean visible = true;
205 public int graphGroup = -1;
207 /** Displayed height of row in pixels */
208 public int height = 0;
210 public int graph = 0;
212 public int graphHeight = 40;
214 public boolean padGaps = false;
216 public static final int NO_GRAPH = 0;
218 public static final int BAR_GRAPH = 1;
220 public static final int LINE_GRAPH = 2;
222 public static final int CUSTOMRENDERER = 4;
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;
248 * @see java.lang.Object#finalize()
251 protected void finalize() throws Throwable
258 public static int getGraphValueFromString(String string)
260 if (string.equalsIgnoreCase("BAR_GRAPH"))
264 else if (string.equalsIgnoreCase("LINE_GRAPH"))
274 // JBPNote: what does this do ?
275 public void ConcenStru(CharSequence RNAannot) throws WUSSParseException
277 bps = Rna.getModeleBP(RNAannot);
281 * Creates a new AlignmentAnnotation object.
284 * short label shown under sequence labels
286 * text displayed on mouseover
288 * set of positional annotation elements
290 public AlignmentAnnotation(String label, String description,
291 Annotation[] annotations)
297 this.description = description;
298 this.annotations = annotations;
300 validateRangeAndDisplay();
304 * Checks if annotation labels represent secondary structures
307 void areLabelsSecondaryStructure()
309 boolean nonSSLabel = false;
311 StringBuffer rnastring = new StringBuffer();
314 for (int i = 0; i < annotations.length; i++)
316 if (annotations[i] == null)
320 if (annotations[i].secondaryStructure == 'H'
321 || annotations[i].secondaryStructure == 'E')
326 // Check for RNA secondary structure
328 // System.out.println(annotations[i].secondaryStructure);
329 // TODO: 2.8.2 should this ss symbol validation check be a function in
330 // RNA/ResidueProperties ?
331 if (annotations[i].secondaryStructure == '('
332 || annotations[i].secondaryStructure == '['
333 || annotations[i].secondaryStructure == '<'
334 || annotations[i].secondaryStructure == '{'
335 || annotations[i].secondaryStructure == 'A'
336 || annotations[i].secondaryStructure == 'B'
337 || annotations[i].secondaryStructure == 'C'
338 || annotations[i].secondaryStructure == 'D'
339 || annotations[i].secondaryStructure == 'E'
340 || annotations[i].secondaryStructure == 'F'
341 || annotations[i].secondaryStructure == 'G'
342 || annotations[i].secondaryStructure == 'H'
343 || annotations[i].secondaryStructure == 'I'
344 || annotations[i].secondaryStructure == 'J'
345 || annotations[i].secondaryStructure == 'K'
346 || annotations[i].secondaryStructure == 'L'
347 || annotations[i].secondaryStructure == 'M'
348 || annotations[i].secondaryStructure == 'N'
349 || annotations[i].secondaryStructure == 'O'
350 || annotations[i].secondaryStructure == 'P'
351 || annotations[i].secondaryStructure == 'Q'
352 || annotations[i].secondaryStructure == 'R'
353 || annotations[i].secondaryStructure == 'S'
354 || annotations[i].secondaryStructure == 'T'
355 || annotations[i].secondaryStructure == 'U'
356 || annotations[i].secondaryStructure == 'V'
357 || annotations[i].secondaryStructure == 'W'
358 || annotations[i].secondaryStructure == 'X'
359 || annotations[i].secondaryStructure == 'Y'
360 || annotations[i].secondaryStructure == 'Z')
367 // System.out.println("displaychar " + annotations[i].displayCharacter);
369 if (annotations[i].displayCharacter == null
370 || annotations[i].displayCharacter.length() == 0)
372 rnastring.append('.');
375 if (annotations[i].displayCharacter.length() == 1)
377 firstChar = annotations[i].displayCharacter.charAt(0);
378 // check to see if it looks like a sequence or is secondary structure
380 if (annotations[i].secondaryStructure != ' '
383 // Uncomment to only catch case where
384 // displayCharacter==secondary
386 // to correctly redisplay SS annotation imported from Stockholm,
387 // exported to JalviewXML and read back in again.
389 // annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure
424 && firstChar < jalview.schemes.ResidueProperties.aaIndex.length)
426 if (jalview.schemes.ResidueProperties.aaIndex[firstChar] < 23) // TODO:
439 rnastring.append(annotations[i].displayCharacter.charAt(1));
442 if (annotations[i].displayCharacter.length() > 0)
451 for (int j = 0; j < annotations.length; j++)
453 if (annotations[j] != null
454 && annotations[j].secondaryStructure != ' ')
456 annotations[j].displayCharacter = String
457 .valueOf(annotations[j].secondaryStructure);
458 annotations[j].secondaryStructure = ' ';
467 _updateRnaSecStr(new AnnotCharSequence());
473 * flyweight access to positions in the alignment annotation row for RNA
479 private class AnnotCharSequence implements CharSequence
485 public AnnotCharSequence()
487 this(0, annotations.length);
490 AnnotCharSequence(int start, int end)
497 public CharSequence subSequence(int start, int end)
499 return new AnnotCharSequence(offset + start, offset + end);
509 public char charAt(int index)
511 return ((index + offset < 0) || (index + offset) >= max
512 || annotations[index + offset] == null
513 || (annotations[index + offset].secondaryStructure <= ' ') ? ' '
514 : annotations[index + offset].displayCharacter == null
515 || annotations[index + offset].displayCharacter
516 .length() == 0 ? annotations[index + offset].secondaryStructure
517 : annotations[index + offset].displayCharacter
522 public String toString()
524 char[] string = new char[max - offset];
525 int mx = annotations.length;
527 for (int i = offset; i < mx; i++)
529 string[i] = (annotations[i] == null || (annotations[i].secondaryStructure <= 32)) ? ' '
530 : (annotations[i].displayCharacter == null
531 || annotations[i].displayCharacter.length() == 0 ? annotations[i].secondaryStructure
532 : annotations[i].displayCharacter.charAt(0));
534 return new String(string);
538 private long _lastrnaannot = -1;
540 public String getRNAStruc()
544 String rnastruc = new AnnotCharSequence().toString();
545 if (_lastrnaannot != rnastruc.hashCode())
547 // ensure rna structure contacts are up to date
548 _lastrnaannot = rnastruc.hashCode();
549 _updateRnaSecStr(rnastruc);
557 * Creates a new AlignmentAnnotation object.
572 public AlignmentAnnotation(String label, String description,
573 Annotation[] annotations, float min, float max, int graphType)
576 // graphs are not editable
577 editable = graphType == 0;
580 this.description = description;
581 this.annotations = annotations;
585 validateRangeAndDisplay();
589 * checks graphMin and graphMax, secondary structure symbols, sets graphType
590 * appropriately, sets null labels to the empty string if appropriate.
592 public void validateRangeAndDisplay()
595 if (annotations == null)
597 visible = false; // try to prevent renderer from displaying.
598 invalidrnastruc = -1;
599 return; // this is a non-annotation row annotation - ie a sequence score.
602 int graphType = graph;
603 float min = graphMin;
604 float max = graphMax;
605 boolean drawValues = true;
610 for (int i = 0; i < annotations.length; i++)
612 if (annotations[i] == null)
617 if (drawValues && annotations[i].displayCharacter != null
618 && annotations[i].displayCharacter.length() > 1)
623 if (annotations[i].value > max)
625 max = annotations[i].value;
628 if (annotations[i].value < min)
630 min = annotations[i].value;
632 if (_linecolour == null && annotations[i].colour != null)
634 _linecolour = annotations[i].colour;
637 // ensure zero is origin for min/max ranges on only one side of zero
654 areLabelsSecondaryStructure();
656 if (!drawValues && graphType != NO_GRAPH)
658 for (int i = 0; i < annotations.length; i++)
660 if (annotations[i] != null)
662 annotations[i].displayCharacter = "";
669 * Copy constructor creates a new independent annotation row with the same
670 * associated sequenceRef
674 public AlignmentAnnotation(AlignmentAnnotation annotation)
677 this.label = new String(annotation.label);
678 if (annotation.description != null)
680 this.description = new String(annotation.description);
682 this.graphMin = annotation.graphMin;
683 this.graphMax = annotation.graphMax;
684 this.graph = annotation.graph;
685 this.graphHeight = annotation.graphHeight;
686 this.graphGroup = annotation.graphGroup;
687 this.groupRef = annotation.groupRef;
688 this.editable = annotation.editable;
689 this.autoCalculated = annotation.autoCalculated;
690 this.hasIcons = annotation.hasIcons;
691 this.hasText = annotation.hasText;
692 this.height = annotation.height;
693 this.label = annotation.label;
694 this.padGaps = annotation.padGaps;
695 this.visible = annotation.visible;
696 this.centreColLabels = annotation.centreColLabels;
697 this.scaleColLabel = annotation.scaleColLabel;
698 this.showAllColLabels = annotation.showAllColLabels;
699 this.calcId = annotation.calcId;
700 if (annotation.properties != null)
702 properties = new HashMap<String, String>();
703 for (Map.Entry<String, String> val : annotation.properties.entrySet())
705 properties.put(val.getKey(), val.getValue());
708 if (this.hasScore = annotation.hasScore)
710 this.score = annotation.score;
712 if (annotation.threshold != null)
714 threshold = new GraphLine(annotation.threshold);
716 Annotation[] ann = annotation.annotations;
717 if (annotation.annotations != null)
719 this.annotations = new Annotation[ann.length];
720 for (int i = 0; i < ann.length; i++)
724 annotations[i] = new Annotation(ann[i]);
725 if (_linecolour != null)
727 _linecolour = annotations[i].colour;
732 if (annotation.sequenceRef != null)
734 this.sequenceRef = annotation.sequenceRef;
735 if (annotation.sequenceMapping != null)
738 sequenceMapping = new HashMap<Integer, Annotation>();
739 Iterator<Integer> pos = annotation.sequenceMapping.keySet()
741 while (pos.hasNext())
743 // could optimise this!
745 Annotation a = annotation.sequenceMapping.get(p);
752 for (int i = 0; i < ann.length; i++)
756 sequenceMapping.put(p, annotations[i]);
764 this.sequenceMapping = null;
767 // TODO: check if we need to do this: JAL-952
768 // if (this.isrna=annotation.isrna)
770 // _rnasecstr=new SequenceFeature[annotation._rnasecstr];
772 validateRangeAndDisplay(); // construct hashcodes, etc.
776 * clip the annotation to the columns given by startRes and endRes (inclusive)
777 * and prune any existing sequenceMapping to just those columns.
782 public void restrict(int startRes, int endRes)
784 if (annotations == null)
793 if (startRes >= annotations.length)
795 startRes = annotations.length - 1;
797 if (endRes >= annotations.length)
799 endRes = annotations.length - 1;
801 if (annotations == null)
805 Annotation[] temp = new Annotation[endRes - startRes + 1];
806 if (startRes < annotations.length)
808 System.arraycopy(annotations, startRes, temp, 0, endRes - startRes
811 if (sequenceRef != null)
813 // Clip the mapping, if it exists.
814 int spos = sequenceRef.findPosition(startRes);
815 int epos = sequenceRef.findPosition(endRes);
816 if (sequenceMapping != null)
818 Map<Integer, Annotation> newmapping = new HashMap<Integer, Annotation>();
819 Iterator<Integer> e = sequenceMapping.keySet().iterator();
822 Integer pos = e.next();
823 if (pos.intValue() >= spos && pos.intValue() <= epos)
825 newmapping.put(pos, sequenceMapping.get(pos));
828 sequenceMapping.clear();
829 sequenceMapping = newmapping;
836 * set the annotation row to be at least length Annotations
839 * minimum number of columns required in the annotation row
840 * @return false if the annotation row is greater than length
842 public boolean padAnnotation(int length)
844 if (annotations == null)
846 return true; // annotation row is correct - null == not visible and
849 if (annotations.length < length)
851 Annotation[] na = new Annotation[length];
852 System.arraycopy(annotations, 0, na, 0, annotations.length);
856 return annotations.length > length;
863 * @return DOCUMENT ME!
866 public String toString()
868 StringBuilder buffer = new StringBuilder(256);
870 for (int i = 0; i < annotations.length; i++)
872 if (annotations[i] != null)
876 buffer.append(annotations[i].value);
880 buffer.append(annotations[i].secondaryStructure);
884 buffer.append(annotations[i].displayCharacter);
890 // TODO: remove disgusting hack for 'special' treatment of consensus line.
891 if (label.indexOf("Consensus") == 0)
895 for (int i = 0; i < annotations.length; i++)
897 if (annotations[i] != null)
899 buffer.append(annotations[i].description);
906 return buffer.toString();
909 public void setThreshold(GraphLine line)
914 public GraphLine getThreshold()
920 * Attach the annotation to seqRef, starting from startRes position. If
921 * alreadyMapped is true then the indices of the annotation[] array are
922 * sequence positions rather than alignment column positions.
926 * @param alreadyMapped
928 public void createSequenceMapping(SequenceI seqRef, int startRes,
929 boolean alreadyMapped)
936 sequenceRef = seqRef;
937 if (annotations == null)
941 sequenceMapping = new HashMap<Integer, Annotation>();
945 for (int i = 0; i < annotations.length; i++)
947 if (annotations[i] != null)
951 seqPos = seqRef.findPosition(i);
955 seqPos = i + startRes;
958 sequenceMapping.put(new Integer(seqPos), annotations[i]);
965 * When positional annotation and a sequence reference is present, clears and
966 * resizes the annotations array to the current alignment width, and adds
967 * annotation according to aligned positions of the sequenceRef given by
970 public void adjustForAlignment()
972 if (sequenceRef == null)
977 if (annotations == null)
982 int a = 0, aSize = sequenceRef.getLength();
991 Annotation[] temp = new Annotation[aSize];
993 if (sequenceMapping != null)
995 for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++)
997 index = new Integer(a);
998 Annotation annot = sequenceMapping.get(index);
1001 position = sequenceRef.findIndex(a) - 1;
1003 temp[position] = annot;
1011 * remove any null entries in annotation row and return the number of non-null
1012 * annotation elements.
1016 public int compactAnnotationArray()
1018 int i = 0, iSize = annotations.length;
1021 if (annotations[i] == null)
1025 System.arraycopy(annotations, i + 1, annotations, i, iSize - i
1035 Annotation[] ann = annotations;
1036 annotations = new Annotation[i];
1037 System.arraycopy(ann, 0, annotations, 0, i);
1043 * Associate this annotation with the aligned residues of a particular
1044 * sequence. sequenceMapping will be updated in the following way: null
1045 * sequenceI - existing mapping will be discarded but annotations left in
1046 * mapped positions. valid sequenceI not equal to current sequenceRef: mapping
1047 * is discarded and rebuilt assuming 1:1 correspondence TODO: overload with
1048 * parameter to specify correspondence between current and new sequenceRef
1052 public void setSequenceRef(SequenceI sequenceI)
1054 if (sequenceI != null)
1056 if (sequenceRef != null)
1058 boolean rIsDs = sequenceRef.getDatasetSequence() == null, tIsDs = sequenceI
1059 .getDatasetSequence() == null;
1060 if (sequenceRef != sequenceI
1061 && (rIsDs && !tIsDs && sequenceRef != sequenceI
1062 .getDatasetSequence())
1063 && (!rIsDs && tIsDs && sequenceRef.getDatasetSequence() != sequenceI)
1064 && (!rIsDs && !tIsDs && sequenceRef.getDatasetSequence() != sequenceI
1065 .getDatasetSequence())
1066 && !sequenceRef.equals(sequenceI))
1068 // if sequenceRef isn't intersecting with sequenceI
1069 // throw away old mapping and reconstruct.
1071 if (sequenceMapping != null)
1073 sequenceMapping = null;
1074 // compactAnnotationArray();
1076 createSequenceMapping(sequenceI, 1, true);
1077 adjustForAlignment();
1081 // Mapping carried over
1082 sequenceRef = sequenceI;
1087 // No mapping exists
1088 createSequenceMapping(sequenceI, 1, true);
1089 adjustForAlignment();
1094 // throw away the mapping without compacting.
1095 sequenceMapping = null;
1103 public double getScore()
1112 public void setScore(double score)
1120 * @return true if annotation has an associated score
1122 public boolean hasScore()
1124 return hasScore || !Double.isNaN(score);
1128 * Score only annotation
1131 * @param description
1134 public AlignmentAnnotation(String label, String description, double score)
1136 this(label, description, null);
1141 * copy constructor with edit based on the hidden columns marked in colSel
1143 * @param alignmentAnnotation
1146 public AlignmentAnnotation(AlignmentAnnotation alignmentAnnotation,
1147 ColumnSelection colSel)
1149 this(alignmentAnnotation);
1150 if (annotations == null)
1154 colSel.makeVisibleAnnotation(this);
1157 public void setPadGaps(boolean padgaps, char gapchar)
1159 this.padGaps = padgaps;
1163 for (int i = 0; i < annotations.length; i++)
1165 if (annotations[i] == null)
1167 annotations[i] = new Annotation(String.valueOf(gapchar), null,
1170 else if (annotations[i].displayCharacter == null
1171 || annotations[i].displayCharacter.equals(" "))
1173 annotations[i].displayCharacter = String.valueOf(gapchar);
1180 * format description string for display
1183 * @return Get the annotation description string optionally prefixed by
1184 * associated sequence name (if any)
1186 public String getDescription(boolean seqname)
1188 if (seqname && this.sequenceRef != null)
1190 int i = description.toLowerCase().indexOf("<html>");
1193 // move the html tag to before the sequence reference.
1194 return "<html>" + sequenceRef.getName() + " : "
1195 + description.substring(i + 6);
1197 return sequenceRef.getName() + " : " + description;
1202 public boolean isValidStruc()
1204 return invalidrnastruc == -1;
1207 public long getInvalidStrucPos()
1209 return invalidrnastruc;
1213 * machine readable ID string indicating what generated this annotation
1215 protected String calcId = "";
1218 * properties associated with the calcId
1220 protected Map<String, String> properties = new HashMap<String, String>();
1223 * base colour for line graphs. If null, will be set automatically by
1224 * searching the alignment annotation
1226 public java.awt.Color _linecolour;
1228 public String getCalcId()
1233 public void setCalcId(String calcId)
1235 this.calcId = calcId;
1238 public boolean isRNA()
1244 * transfer annotation to the given sequence using the given mapping from the
1245 * current positions or an existing sequence mapping
1249 * map involving sq as To or From
1251 public void liftOver(SequenceI sq, Mapping sp2sq)
1253 if (sp2sq.getMappedWidth() != sp2sq.getWidth())
1255 // TODO: employ getWord/MappedWord to transfer annotation between cDNA and
1256 // Protein reference frames
1258 "liftOver currently not implemented for transfer of annotation between different types of seqeunce");
1260 boolean mapIsTo = (sp2sq != null) ? (sp2sq.getTo() == sq || sp2sq
1261 .getTo() == sq.getDatasetSequence()) : false;
1263 // TODO build a better annotation element map and get rid of annotations[]
1264 Map<Integer, Annotation> mapForsq = new HashMap<Integer, Annotation>();
1265 if (sequenceMapping != null)
1269 for (Entry<Integer, Annotation> ie : sequenceMapping.entrySet())
1271 Integer mpos = Integer.valueOf(mapIsTo ? sp2sq
1272 .getMappedPosition(ie.getKey()) : sp2sq.getPosition(ie
1274 if (mpos >= sq.getStart() && mpos <= sq.getEnd())
1276 mapForsq.put(mpos, ie.getValue());
1279 sequenceMapping = mapForsq;
1281 adjustForAlignment();
1291 * like liftOver but more general.
1293 * Takes an array of int pairs that will be used to update the internal
1294 * sequenceMapping and so shuffle the annotated positions
1297 * - new sequence reference for the annotation row - if null,
1298 * sequenceRef is left unchanged
1300 * array of ints containing corresponding positions
1302 * - column for current coordinate system (-1 for index+1)
1304 * - column for destination coordinate system (-1 for index+1)
1306 * - offset added to index when referencing either coordinate system
1307 * @note no checks are made as to whether from and/or to are sensible
1308 * @note caller should add the remapped annotation to newref if they have not
1311 public void remap(SequenceI newref, HashMap<Integer, int[]> mapping,
1312 int from, int to, int idxoffset)
1314 if (mapping != null)
1316 Map<Integer, Annotation> old = sequenceMapping;
1317 Map<Integer, Annotation> remap = new HashMap<Integer, Annotation>();
1319 for (int mp[] : mapping.values())
1325 Annotation ann = null;
1328 ann = sequenceMapping.get(Integer.valueOf(idxoffset + index));
1332 if (mp != null && mp.length > from)
1334 ann = sequenceMapping.get(Integer.valueOf(mp[from]));
1341 remap.put(Integer.valueOf(idxoffset + index), ann);
1345 if (to > -1 && to < mp.length)
1347 remap.put(Integer.valueOf(mp[to]), ann);
1352 sequenceMapping = remap;
1356 sequenceRef = newref;
1358 adjustForAlignment();
1362 public String getProperty(String property)
1364 if (properties == null)
1368 return properties.get(property);
1371 public void setProperty(String property, String value)
1373 if (properties == null)
1375 properties = new HashMap<String, String>();
1377 properties.put(property, value);
1380 public boolean hasProperties()
1382 return properties != null && properties.size() > 0;
1385 public Collection<String> getProperties()
1387 if (properties == null)
1389 return Collections.emptyList();
1391 return properties.keySet();
1395 * Returns the Annotation for the given sequence position (base 1) if any,
1401 public Annotation getAnnotationForPosition(int position)
1403 return sequenceMapping == null ? null : sequenceMapping.get(position);
1408 * Set the id to "ann" followed by a counter that increments so as to be
1409 * unique for the lifetime of the JVM
1411 protected final void setAnnotationId()
1413 this.annotationId = ANNOTATION_ID_PREFIX + Long.toString(nextId());
1417 * Returns the match for the last unmatched opening RNA helix pair symbol
1418 * preceding the given column, or '(' if nothing found to match.
1423 public String getDefaultRnaHelixSymbol(int column)
1425 String result = "(";
1426 if (annotations == null)
1432 * for each preceding column, if it contains an open bracket,
1433 * count whether it is still unmatched at column, if so return its pair
1434 * (likely faster than the fancy alternative using stacks)
1436 for (int col = column - 1; col >= 0; col--)
1438 Annotation annotation = annotations[col];
1439 if (annotation == null)
1443 String displayed = annotation.displayCharacter;
1444 if (displayed == null || displayed.length() != 1)
1448 char symbol = displayed.charAt(0);
1449 if (!Rna.isOpeningParenthesis(symbol))
1455 * found an opening bracket symbol
1456 * count (closing-opening) symbols of this type that follow it,
1457 * up to and excluding the target column; if the count is less
1458 * than 1, the opening bracket is unmatched, so return its match
1460 String closer = String.valueOf(Rna
1461 .getMatchingClosingParenthesis(symbol));
1462 String opener = String.valueOf(symbol);
1464 for (int j = col + 1; j < column; j++)
1466 if (annotations[j] != null)
1468 String s = annotations[j].displayCharacter;
1469 if (closer.equals(s))
1473 else if (opener.equals(s))
1487 protected static synchronized long nextId()