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
99 * @param rnaAnnotation
101 private void _updateRnaSecStr(CharSequence rnaAnnotation)
105 _rnasecstr = Rna.getHelixMap(rnaAnnotation);
106 invalidrnastruc = -1;
107 } catch (WUSSParseException px)
109 // DEBUG System.out.println(px);
110 invalidrnastruc = px.getProblemPos();
112 if (invalidrnastruc > -1)
117 if (_rnasecstr != null && _rnasecstr.length > 0)
119 // show all the RNA secondary structure annotation symbols.
121 showAllColLabels = true;
122 scaleColLabel = true;
125 // System.out.println("featuregroup " + _rnasecstr[0].getFeatureGroup());
129 private void _markRnaHelices()
132 // Figure out number of helices
133 // Length of rnasecstr is the number of pairs of positions that base pair
134 // with each other in the secondary structure
135 for (int x = 0; x < _rnasecstr.length; x++)
139 * System.out.println(this.annotation._rnasecstr[x] + " Begin" +
140 * this.annotation._rnasecstr[x].getBegin());
142 // System.out.println(this.annotation._rnasecstr[x].getFeatureGroup());
146 val = Integer.valueOf(_rnasecstr[x].getFeatureGroup());
151 } catch (NumberFormatException q)
156 annotations[_rnasecstr[x].getBegin()].value = val;
157 annotations[_rnasecstr[x].getEnd()].value = val;
159 // annotations[_rnasecstr[x].getBegin()].displayCharacter = "" + val;
160 // annotations[_rnasecstr[x].getEnd()].displayCharacter = "" + val;
166 * map of positions in the associated annotation
168 private Map<Integer, Annotation> sequenceMapping;
171 * lower range for quantitative data
173 public float graphMin;
176 * Upper range for quantitative data
178 public float graphMax;
181 * Score associated with label and description.
183 public double score = Double.NaN;
186 * flag indicating if annotation has a score.
188 public boolean hasScore = false;
190 public GraphLine threshold;
192 // Graphical hints and tips
194 /** Can this row be edited by the user ? */
195 public boolean editable = false;
197 /** Indicates if annotation has a graphical symbol track */
198 public boolean hasIcons; //
200 /** Indicates if annotation has a text character label */
201 public boolean hasText;
203 /** is the row visible */
204 public boolean visible = true;
206 public int graphGroup = -1;
208 /** Displayed height of row in pixels */
209 public int height = 0;
211 public int graph = 0;
213 public int graphHeight = 40;
215 public boolean padGaps = false;
217 public static final int NO_GRAPH = 0;
219 public static final int BAR_GRAPH = 1;
221 public static final int LINE_GRAPH = 2;
223 public boolean belowAlignment = true;
225 public SequenceGroup groupRef = null;
228 * display every column label, even if there is a row of identical labels
230 public boolean showAllColLabels = false;
233 * scale the column label to fit within the alignment column.
235 public boolean scaleColLabel = false;
238 * centre the column labels relative to the alignment column
240 public boolean centreColLabels = false;
242 private boolean isrna;
247 * @see java.lang.Object#finalize()
250 protected void finalize() throws Throwable
257 public static int getGraphValueFromString(String string)
259 if (string.equalsIgnoreCase("BAR_GRAPH"))
263 else if (string.equalsIgnoreCase("LINE_GRAPH"))
274 * Creates a new AlignmentAnnotation object.
277 * short label shown under sequence labels
279 * text displayed on mouseover
281 * set of positional annotation elements
283 public AlignmentAnnotation(String label, String description,
284 Annotation[] annotations)
290 this.description = description;
291 this.annotations = annotations;
293 validateRangeAndDisplay();
297 * Checks if annotation labels represent secondary structures
300 void areLabelsSecondaryStructure()
302 boolean nonSSLabel = false;
304 StringBuffer rnastring = new StringBuffer();
307 for (int i = 0; i < annotations.length; i++)
309 if (annotations[i] == null)
313 if (annotations[i].secondaryStructure == 'H'
314 || annotations[i].secondaryStructure == 'E')
319 // Check for RNA secondary structure
321 // System.out.println(annotations[i].secondaryStructure);
322 // TODO: 2.8.2 should this ss symbol validation check be a function in
323 // RNA/ResidueProperties ?
324 if (annotations[i].secondaryStructure == '('
325 || annotations[i].secondaryStructure == '['
326 || annotations[i].secondaryStructure == '<'
327 || annotations[i].secondaryStructure == '{'
328 || annotations[i].secondaryStructure == 'A'
329 || annotations[i].secondaryStructure == 'B'
330 || annotations[i].secondaryStructure == 'C'
331 || annotations[i].secondaryStructure == 'D'
332 || annotations[i].secondaryStructure == 'E'
333 || annotations[i].secondaryStructure == 'F'
334 || annotations[i].secondaryStructure == 'G'
335 || annotations[i].secondaryStructure == 'H'
336 || annotations[i].secondaryStructure == 'I'
337 || annotations[i].secondaryStructure == 'J'
338 || annotations[i].secondaryStructure == 'K'
339 || annotations[i].secondaryStructure == 'L'
340 || annotations[i].secondaryStructure == 'M'
341 || annotations[i].secondaryStructure == 'N'
342 || annotations[i].secondaryStructure == 'O'
343 || annotations[i].secondaryStructure == 'P'
344 || annotations[i].secondaryStructure == 'Q'
345 || annotations[i].secondaryStructure == 'R'
346 || annotations[i].secondaryStructure == 'S'
347 || annotations[i].secondaryStructure == 'T'
348 || annotations[i].secondaryStructure == 'U'
349 || annotations[i].secondaryStructure == 'V'
350 || annotations[i].secondaryStructure == 'W'
351 || annotations[i].secondaryStructure == 'X'
352 || annotations[i].secondaryStructure == 'Y'
353 || annotations[i].secondaryStructure == 'Z')
360 // System.out.println("displaychar " + annotations[i].displayCharacter);
362 if (annotations[i].displayCharacter == null
363 || annotations[i].displayCharacter.length() == 0)
365 rnastring.append('.');
368 if (annotations[i].displayCharacter.length() == 1)
370 firstChar = annotations[i].displayCharacter.charAt(0);
371 // check to see if it looks like a sequence or is secondary structure
373 if (annotations[i].secondaryStructure != ' '
376 // Uncomment to only catch case where
377 // displayCharacter==secondary
379 // to correctly redisplay SS annotation imported from Stockholm,
380 // exported to JalviewXML and read back in again.
382 // annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure
417 && firstChar < jalview.schemes.ResidueProperties.aaIndex.length)
419 if (jalview.schemes.ResidueProperties.aaIndex[firstChar] < 23) // TODO:
432 rnastring.append(annotations[i].displayCharacter.charAt(1));
435 if (annotations[i].displayCharacter.length() > 0)
444 for (int j = 0; j < annotations.length; j++)
446 if (annotations[j] != null
447 && annotations[j].secondaryStructure != ' ')
449 annotations[j].displayCharacter = String
450 .valueOf(annotations[j].secondaryStructure);
451 annotations[j].secondaryStructure = ' ';
460 _updateRnaSecStr(new AnnotCharSequence());
466 * flyweight access to positions in the alignment annotation row for RNA
472 private class AnnotCharSequence implements CharSequence
478 public AnnotCharSequence()
480 this(0, annotations.length);
483 AnnotCharSequence(int start, int end)
490 public CharSequence subSequence(int start, int end)
492 return new AnnotCharSequence(offset + start, offset + end);
502 public char charAt(int index)
504 return ((index + offset < 0) || (index + offset) >= max
505 || annotations[index + offset] == null
506 || (annotations[index + offset].secondaryStructure <= ' ') ? ' '
507 : annotations[index + offset].displayCharacter == null
508 || annotations[index + offset].displayCharacter
509 .length() == 0 ? annotations[index + offset].secondaryStructure
510 : annotations[index + offset].displayCharacter
515 public String toString()
517 char[] string = new char[max - offset];
518 int mx = annotations.length;
520 for (int i = offset; i < mx; i++)
522 string[i] = (annotations[i] == null || (annotations[i].secondaryStructure <= 32)) ? ' '
523 : (annotations[i].displayCharacter == null
524 || annotations[i].displayCharacter.length() == 0 ? annotations[i].secondaryStructure
525 : annotations[i].displayCharacter.charAt(0));
527 return new String(string);
531 private long _lastrnaannot = -1;
533 public String getRNAStruc()
537 String rnastruc = new AnnotCharSequence().toString();
538 if (_lastrnaannot != rnastruc.hashCode())
540 // ensure rna structure contacts are up to date
541 _lastrnaannot = rnastruc.hashCode();
542 _updateRnaSecStr(rnastruc);
550 * Creates a new AlignmentAnnotation object.
565 public AlignmentAnnotation(String label, String description,
566 Annotation[] annotations, float min, float max, int graphType)
569 // graphs are not editable
570 editable = graphType == 0;
573 this.description = description;
574 this.annotations = annotations;
578 validateRangeAndDisplay();
582 * checks graphMin and graphMax, secondary structure symbols, sets graphType
583 * appropriately, sets null labels to the empty string if appropriate.
585 public void validateRangeAndDisplay()
588 if (annotations == null)
590 visible = false; // try to prevent renderer from displaying.
591 invalidrnastruc = -1;
592 return; // this is a non-annotation row annotation - ie a sequence score.
595 int graphType = graph;
596 float min = graphMin;
597 float max = graphMax;
598 boolean drawValues = true;
603 for (int i = 0; i < annotations.length; i++)
605 if (annotations[i] == null)
610 if (drawValues && annotations[i].displayCharacter != null
611 && annotations[i].displayCharacter.length() > 1)
616 if (annotations[i].value > max)
618 max = annotations[i].value;
621 if (annotations[i].value < min)
623 min = annotations[i].value;
625 if (_linecolour == null && annotations[i].colour != null)
627 _linecolour = annotations[i].colour;
630 // ensure zero is origin for min/max ranges on only one side of zero
647 areLabelsSecondaryStructure();
649 if (!drawValues && graphType != NO_GRAPH)
651 for (int i = 0; i < annotations.length; i++)
653 if (annotations[i] != null)
655 annotations[i].displayCharacter = "";
662 * Copy constructor creates a new independent annotation row with the same
663 * associated sequenceRef
667 public AlignmentAnnotation(AlignmentAnnotation annotation)
670 this.label = new String(annotation.label);
671 if (annotation.description != null)
673 this.description = new String(annotation.description);
675 this.graphMin = annotation.graphMin;
676 this.graphMax = annotation.graphMax;
677 this.graph = annotation.graph;
678 this.graphHeight = annotation.graphHeight;
679 this.graphGroup = annotation.graphGroup;
680 this.groupRef = annotation.groupRef;
681 this.editable = annotation.editable;
682 this.autoCalculated = annotation.autoCalculated;
683 this.hasIcons = annotation.hasIcons;
684 this.hasText = annotation.hasText;
685 this.height = annotation.height;
686 this.label = annotation.label;
687 this.padGaps = annotation.padGaps;
688 this.visible = annotation.visible;
689 this.centreColLabels = annotation.centreColLabels;
690 this.scaleColLabel = annotation.scaleColLabel;
691 this.showAllColLabels = annotation.showAllColLabels;
692 this.calcId = annotation.calcId;
693 if (annotation.properties != null)
695 properties = new HashMap<String, String>();
696 for (Map.Entry<String, String> val : annotation.properties.entrySet())
698 properties.put(val.getKey(), val.getValue());
701 if (this.hasScore = annotation.hasScore)
703 this.score = annotation.score;
705 if (annotation.threshold != null)
707 threshold = new GraphLine(annotation.threshold);
709 Annotation[] ann = annotation.annotations;
710 if (annotation.annotations != null)
712 this.annotations = new Annotation[ann.length];
713 for (int i = 0; i < ann.length; i++)
717 annotations[i] = new Annotation(ann[i]);
718 if (_linecolour != null)
720 _linecolour = annotations[i].colour;
725 if (annotation.sequenceRef != null)
727 this.sequenceRef = annotation.sequenceRef;
728 if (annotation.sequenceMapping != null)
731 sequenceMapping = new HashMap<Integer, Annotation>();
732 Iterator<Integer> pos = annotation.sequenceMapping.keySet()
734 while (pos.hasNext())
736 // could optimise this!
738 Annotation a = annotation.sequenceMapping.get(p);
745 for (int i = 0; i < ann.length; i++)
749 sequenceMapping.put(p, annotations[i]);
757 this.sequenceMapping = null;
760 // TODO: check if we need to do this: JAL-952
761 // if (this.isrna=annotation.isrna)
763 // _rnasecstr=new SequenceFeature[annotation._rnasecstr];
765 validateRangeAndDisplay(); // construct hashcodes, etc.
769 * clip the annotation to the columns given by startRes and endRes (inclusive)
770 * and prune any existing sequenceMapping to just those columns.
775 public void restrict(int startRes, int endRes)
777 if (annotations == null)
786 if (startRes >= annotations.length)
788 startRes = annotations.length - 1;
790 if (endRes >= annotations.length)
792 endRes = annotations.length - 1;
794 if (annotations == null)
798 Annotation[] temp = new Annotation[endRes - startRes + 1];
799 if (startRes < annotations.length)
801 System.arraycopy(annotations, startRes, temp, 0, endRes - startRes
804 if (sequenceRef != null)
806 // Clip the mapping, if it exists.
807 int spos = sequenceRef.findPosition(startRes);
808 int epos = sequenceRef.findPosition(endRes);
809 if (sequenceMapping != null)
811 Map<Integer, Annotation> newmapping = new HashMap<Integer, Annotation>();
812 Iterator<Integer> e = sequenceMapping.keySet().iterator();
815 Integer pos = e.next();
816 if (pos.intValue() >= spos && pos.intValue() <= epos)
818 newmapping.put(pos, sequenceMapping.get(pos));
821 sequenceMapping.clear();
822 sequenceMapping = newmapping;
829 * set the annotation row to be at least length Annotations
832 * minimum number of columns required in the annotation row
833 * @return false if the annotation row is greater than length
835 public boolean padAnnotation(int length)
837 if (annotations == null)
839 return true; // annotation row is correct - null == not visible and
842 if (annotations.length < length)
844 Annotation[] na = new Annotation[length];
845 System.arraycopy(annotations, 0, na, 0, annotations.length);
849 return annotations.length > length;
856 * @return DOCUMENT ME!
859 public String toString()
861 if (annotations == null)
865 StringBuilder buffer = new StringBuilder(256);
867 for (int i = 0; i < annotations.length; i++)
869 if (annotations[i] != null)
873 buffer.append(annotations[i].value);
877 buffer.append(annotations[i].secondaryStructure);
881 buffer.append(annotations[i].displayCharacter);
887 // TODO: remove disgusting hack for 'special' treatment of consensus line.
888 if (label.indexOf("Consensus") == 0)
892 for (int i = 0; i < annotations.length; i++)
894 if (annotations[i] != null)
896 buffer.append(annotations[i].description);
903 return buffer.toString();
906 public void setThreshold(GraphLine line)
911 public GraphLine getThreshold()
917 * Attach the annotation to seqRef, starting from startRes position. If
918 * alreadyMapped is true then the indices of the annotation[] array are
919 * sequence positions rather than alignment column positions.
923 * @param alreadyMapped
925 public void createSequenceMapping(SequenceI seqRef, int startRes,
926 boolean alreadyMapped)
933 sequenceRef = seqRef;
934 if (annotations == null)
938 sequenceMapping = new HashMap<Integer, Annotation>();
942 for (int i = 0; i < annotations.length; i++)
944 if (annotations[i] != null)
948 seqPos = seqRef.findPosition(i);
952 seqPos = i + startRes;
955 sequenceMapping.put(new Integer(seqPos), annotations[i]);
962 * When positional annotation and a sequence reference is present, clears and
963 * resizes the annotations array to the current alignment width, and adds
964 * annotation according to aligned positions of the sequenceRef given by
967 public void adjustForAlignment()
969 if (sequenceRef == null)
974 if (annotations == null)
979 int a = 0, aSize = sequenceRef.getLength();
988 Annotation[] temp = new Annotation[aSize];
990 if (sequenceMapping != null)
992 for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++)
994 index = new Integer(a);
995 Annotation annot = sequenceMapping.get(index);
998 position = sequenceRef.findIndex(a) - 1;
1000 temp[position] = annot;
1008 * remove any null entries in annotation row and return the number of non-null
1009 * annotation elements.
1013 public int compactAnnotationArray()
1015 int i = 0, iSize = annotations.length;
1018 if (annotations[i] == null)
1022 System.arraycopy(annotations, i + 1, annotations, i, iSize - i
1032 Annotation[] ann = annotations;
1033 annotations = new Annotation[i];
1034 System.arraycopy(ann, 0, annotations, 0, i);
1040 * Associate this annotation with the aligned residues of a particular
1041 * sequence. sequenceMapping will be updated in the following way: null
1042 * sequenceI - existing mapping will be discarded but annotations left in
1043 * mapped positions. valid sequenceI not equal to current sequenceRef: mapping
1044 * is discarded and rebuilt assuming 1:1 correspondence TODO: overload with
1045 * parameter to specify correspondence between current and new sequenceRef
1049 public void setSequenceRef(SequenceI sequenceI)
1051 if (sequenceI != null)
1053 if (sequenceRef != null)
1055 boolean rIsDs = sequenceRef.getDatasetSequence() == null, tIsDs = sequenceI
1056 .getDatasetSequence() == null;
1057 if (sequenceRef != sequenceI
1058 && (rIsDs && !tIsDs && sequenceRef != sequenceI
1059 .getDatasetSequence())
1060 && (!rIsDs && tIsDs && sequenceRef.getDatasetSequence() != sequenceI)
1061 && (!rIsDs && !tIsDs && sequenceRef.getDatasetSequence() != sequenceI
1062 .getDatasetSequence())
1063 && !sequenceRef.equals(sequenceI))
1065 // if sequenceRef isn't intersecting with sequenceI
1066 // throw away old mapping and reconstruct.
1068 if (sequenceMapping != null)
1070 sequenceMapping = null;
1071 // compactAnnotationArray();
1073 createSequenceMapping(sequenceI, 1, true);
1074 adjustForAlignment();
1078 // Mapping carried over
1079 sequenceRef = sequenceI;
1084 // No mapping exists
1085 createSequenceMapping(sequenceI, 1, true);
1086 adjustForAlignment();
1091 // throw away the mapping without compacting.
1092 sequenceMapping = null;
1100 public double getScore()
1109 public void setScore(double score)
1117 * @return true if annotation has an associated score
1119 public boolean hasScore()
1121 return hasScore || !Double.isNaN(score);
1125 * Score only annotation
1128 * @param description
1131 public AlignmentAnnotation(String label, String description, double score)
1133 this(label, description, null);
1138 * copy constructor with edit based on the hidden columns marked in colSel
1140 * @param alignmentAnnotation
1143 public AlignmentAnnotation(AlignmentAnnotation alignmentAnnotation,
1144 HiddenColumns hidden)
1146 this(alignmentAnnotation);
1147 if (annotations == null)
1151 hidden.makeVisibleAnnotation(this);
1154 public void setPadGaps(boolean padgaps, char gapchar)
1156 this.padGaps = padgaps;
1160 for (int i = 0; i < annotations.length; i++)
1162 if (annotations[i] == null)
1164 annotations[i] = new Annotation(String.valueOf(gapchar), null,
1167 else if (annotations[i].displayCharacter == null
1168 || annotations[i].displayCharacter.equals(" "))
1170 annotations[i].displayCharacter = String.valueOf(gapchar);
1177 * format description string for display
1180 * @return Get the annotation description string optionally prefixed by
1181 * associated sequence name (if any)
1183 public String getDescription(boolean seqname)
1185 if (seqname && this.sequenceRef != null)
1187 int i = description.toLowerCase().indexOf("<html>");
1190 // move the html tag to before the sequence reference.
1191 return "<html>" + sequenceRef.getName() + " : "
1192 + description.substring(i + 6);
1194 return sequenceRef.getName() + " : " + description;
1199 public boolean isValidStruc()
1201 return invalidrnastruc == -1;
1204 public long getInvalidStrucPos()
1206 return invalidrnastruc;
1210 * machine readable ID string indicating what generated this annotation
1212 protected String calcId = "";
1215 * properties associated with the calcId
1217 protected Map<String, String> properties = new HashMap<String, String>();
1220 * base colour for line graphs. If null, will be set automatically by
1221 * searching the alignment annotation
1223 public java.awt.Color _linecolour;
1225 public String getCalcId()
1230 public void setCalcId(String calcId)
1232 this.calcId = calcId;
1235 public boolean isRNA()
1241 * transfer annotation to the given sequence using the given mapping from the
1242 * current positions or an existing sequence mapping
1246 * map involving sq as To or From
1248 public void liftOver(SequenceI sq, Mapping sp2sq)
1250 if (sp2sq.getMappedWidth() != sp2sq.getWidth())
1252 // TODO: employ getWord/MappedWord to transfer annotation between cDNA and
1253 // Protein reference frames
1255 "liftOver currently not implemented for transfer of annotation between different types of seqeunce");
1257 boolean mapIsTo = (sp2sq != null) ? (sp2sq.getTo() == sq || sp2sq
1258 .getTo() == sq.getDatasetSequence()) : false;
1260 // TODO build a better annotation element map and get rid of annotations[]
1261 Map<Integer, Annotation> mapForsq = new HashMap<Integer, Annotation>();
1262 if (sequenceMapping != null)
1266 for (Entry<Integer, Annotation> ie : sequenceMapping.entrySet())
1268 Integer mpos = Integer.valueOf(mapIsTo ? sp2sq
1269 .getMappedPosition(ie.getKey()) : sp2sq.getPosition(ie
1271 if (mpos >= sq.getStart() && mpos <= sq.getEnd())
1273 mapForsq.put(mpos, ie.getValue());
1276 sequenceMapping = mapForsq;
1278 adjustForAlignment();
1288 * like liftOver but more general.
1290 * Takes an array of int pairs that will be used to update the internal
1291 * sequenceMapping and so shuffle the annotated positions
1294 * - new sequence reference for the annotation row - if null,
1295 * sequenceRef is left unchanged
1297 * array of ints containing corresponding positions
1299 * - column for current coordinate system (-1 for index+1)
1301 * - column for destination coordinate system (-1 for index+1)
1303 * - offset added to index when referencing either coordinate system
1304 * @note no checks are made as to whether from and/or to are sensible
1305 * @note caller should add the remapped annotation to newref if they have not
1308 public void remap(SequenceI newref, HashMap<Integer, int[]> mapping,
1309 int from, int to, int idxoffset)
1311 if (mapping != null)
1313 Map<Integer, Annotation> old = sequenceMapping;
1314 Map<Integer, Annotation> remap = new HashMap<Integer, Annotation>();
1316 for (int mp[] : mapping.values())
1322 Annotation ann = null;
1325 ann = sequenceMapping.get(Integer.valueOf(idxoffset + index));
1329 if (mp != null && mp.length > from)
1331 ann = sequenceMapping.get(Integer.valueOf(mp[from]));
1338 remap.put(Integer.valueOf(idxoffset + index), ann);
1342 if (to > -1 && to < mp.length)
1344 remap.put(Integer.valueOf(mp[to]), ann);
1349 sequenceMapping = remap;
1353 sequenceRef = newref;
1355 adjustForAlignment();
1359 public String getProperty(String property)
1361 if (properties == null)
1365 return properties.get(property);
1368 public void setProperty(String property, String value)
1370 if (properties == null)
1372 properties = new HashMap<String, String>();
1374 properties.put(property, value);
1377 public boolean hasProperties()
1379 return properties != null && properties.size() > 0;
1382 public Collection<String> getProperties()
1384 if (properties == null)
1386 return Collections.emptyList();
1388 return properties.keySet();
1392 * Returns the Annotation for the given sequence position (base 1) if any,
1398 public Annotation getAnnotationForPosition(int position)
1400 return sequenceMapping == null ? null : sequenceMapping.get(position);
1405 * Set the id to "ann" followed by a counter that increments so as to be
1406 * unique for the lifetime of the JVM
1408 protected final void setAnnotationId()
1410 this.annotationId = ANNOTATION_ID_PREFIX + Long.toString(nextId());
1414 * Returns the match for the last unmatched opening RNA helix pair symbol
1415 * preceding the given column, or '(' if nothing found to match.
1420 public String getDefaultRnaHelixSymbol(int column)
1422 String result = "(";
1423 if (annotations == null)
1429 * for each preceding column, if it contains an open bracket,
1430 * count whether it is still unmatched at column, if so return its pair
1431 * (likely faster than the fancy alternative using stacks)
1433 for (int col = column - 1; col >= 0; col--)
1435 Annotation annotation = annotations[col];
1436 if (annotation == null)
1440 String displayed = annotation.displayCharacter;
1441 if (displayed == null || displayed.length() != 1)
1445 char symbol = displayed.charAt(0);
1446 if (!Rna.isOpeningParenthesis(symbol))
1452 * found an opening bracket symbol
1453 * count (closing-opening) symbols of this type that follow it,
1454 * up to and excluding the target column; if the count is less
1455 * than 1, the opening bracket is unmatched, so return its match
1457 String closer = String.valueOf(Rna
1458 .getMatchingClosingParenthesis(symbol));
1459 String opener = String.valueOf(symbol);
1461 for (int j = col + 1; j < column; j++)
1463 if (annotations[j] != null)
1465 String s = annotations[j].displayCharacter;
1466 if (closer.equals(s))
1470 else if (opener.equals(s))
1484 protected static synchronized long nextId()
1491 * @return true for rows that have a range of values in their annotation set
1493 public boolean isQuantitative()
1495 return graphMin < graphMax;