+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.datamodel;
-
-import jalview.analysis.Rna;
-import jalview.analysis.SecStrConsensus.SimpleBP;
-import jalview.analysis.WUSSParseException;
-import jalview.util.MapList;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class AlignmentAnnotation
-{
- private static final String ANNOTATION_ID_PREFIX = "ann";
-
- /*
- * Identifers for different types of profile data
- */
- public static final int SEQUENCE_PROFILE = 0;
-
- public static final int STRUCTURE_PROFILE = 1;
-
- public static final int CDNA_PROFILE = 2;
-
- private static long counter = 0;
-
- /**
- * If true, this annotations is calculated every edit, eg consensus, quality
- * or conservation graphs
- */
- public boolean autoCalculated = false;
-
- /**
- * unique ID for this annotation, used to match up the same annotation row
- * shown in multiple views and alignments
- */
- public String annotationId;
-
- /**
- * the sequence this annotation is associated with (or null)
- */
- public SequenceI sequenceRef;
-
- /** label shown in dropdown menus and in the annotation label area */
- public String label;
-
- /** longer description text shown as a tooltip */
- public String description;
-
- /** Array of annotations placed in the current coordinate system */
- public Annotation[] annotations;
-
- public List<SimpleBP> bps = null;
-
- /**
- * RNA secondary structure contact positions
- */
- public SequenceFeature[] _rnasecstr = null;
-
- /**
- * position of annotation resulting in invalid WUSS parsing or -1. -2 means
- * there was no RNA structure in this annotation
- */
- private long invalidrnastruc = -2;
-
- /**
- * Updates the _rnasecstr field Determines the positions that base pair and
- * the positions of helices based on secondary structure from a Stockholm file
- *
- * @param rnaAnnotation
- */
- private void _updateRnaSecStr(CharSequence rnaAnnotation)
- {
- try
- {
- _rnasecstr = Rna.getHelixMap(rnaAnnotation);
- invalidrnastruc = -1;
- } catch (WUSSParseException px)
- {
- // DEBUG System.out.println(px);
- invalidrnastruc = px.getProblemPos();
- }
- if (invalidrnastruc > -1)
- {
- return;
- }
-
- if (_rnasecstr != null && _rnasecstr.length > 0)
- {
- // show all the RNA secondary structure annotation symbols.
- isrna = true;
- showAllColLabels = true;
- scaleColLabel = true;
- _markRnaHelices();
- }
- // System.out.println("featuregroup " + _rnasecstr[0].getFeatureGroup());
-
- }
-
- private void _markRnaHelices()
- {
- int mxval = 0;
- // Figure out number of helices
- // Length of rnasecstr is the number of pairs of positions that base pair
- // with each other in the secondary structure
- for (int x = 0; x < _rnasecstr.length; x++)
- {
-
- /*
- * System.out.println(this.annotation._rnasecstr[x] + " Begin" +
- * this.annotation._rnasecstr[x].getBegin());
- */
- // System.out.println(this.annotation._rnasecstr[x].getFeatureGroup());
- int val = 0;
- try
- {
- val = Integer.valueOf(_rnasecstr[x].getFeatureGroup());
- if (mxval < val)
- {
- mxval = val;
- }
- } catch (NumberFormatException q)
- {
- }
- ;
-
- annotations[_rnasecstr[x].getBegin()].value = val;
- annotations[_rnasecstr[x].getEnd()].value = val;
-
- // annotations[_rnasecstr[x].getBegin()].displayCharacter = "" + val;
- // annotations[_rnasecstr[x].getEnd()].displayCharacter = "" + val;
- }
- setScore(mxval);
- }
-
- /**
- * Get the RNA Secondary Structure SequenceFeature Array if present
- */
- public SequenceFeature[] getRnaSecondaryStructure()
- {
- return this._rnasecstr;
- }
-
- /**
- * Check the RNA Secondary Structure is equivalent to one in given
- * AlignmentAnnotation param
- */
- public boolean rnaSecondaryStructureEquivalent(AlignmentAnnotation that)
- {
- return rnaSecondaryStructureEquivalent(that, true);
- }
-
- public boolean rnaSecondaryStructureEquivalent(AlignmentAnnotation that, boolean compareType)
- {
- SequenceFeature[] thisSfArray = this.getRnaSecondaryStructure();
- SequenceFeature[] thatSfArray = that.getRnaSecondaryStructure();
- if (thisSfArray == null || thatSfArray == null)
- {
- return thisSfArray == null && thatSfArray == null;
- }
- if (thisSfArray.length != thatSfArray.length)
- {
- return false;
- }
- Arrays.sort(thisSfArray, new SFSortByEnd()); // probably already sorted
- // like this
- Arrays.sort(thatSfArray, new SFSortByEnd()); // probably already sorted
- // like this
- for (int i=0; i < thisSfArray.length; i++) {
- SequenceFeature thisSf = thisSfArray[i];
- SequenceFeature thatSf = thatSfArray[i];
- if (compareType) {
- if (thisSf.getType() == null || thatSf.getType() == null) {
- if (thisSf.getType() == null && thatSf.getType() == null) {
- continue;
- } else {
- return false;
- }
- }
- if (! thisSf.getType().equals(thatSf.getType())) {
- return false;
- }
- }
- if (!(thisSf.getBegin() == thatSf.getBegin()
- && thisSf.getEnd() == thatSf.getEnd()))
- {
- return false;
- }
- }
- return true;
-
- }
-
- /**
- * map of positions in the associated annotation
- */
- private Map<Integer, Annotation> sequenceMapping;
-
- /**
- * lower range for quantitative data
- */
- public float graphMin;
-
- /**
- * Upper range for quantitative data
- */
- public float graphMax;
-
- /**
- * Score associated with label and description.
- */
- public double score = Double.NaN;
-
- /**
- * flag indicating if annotation has a score.
- */
- public boolean hasScore = false;
-
- public GraphLine threshold;
-
- // Graphical hints and tips
-
- /** Can this row be edited by the user ? */
- public boolean editable = false;
-
- /** Indicates if annotation has a graphical symbol track */
- public boolean hasIcons; //
-
- /** Indicates if annotation has a text character label */
- public boolean hasText;
-
- /** is the row visible */
- public boolean visible = true;
-
- public int graphGroup = -1;
-
- /** Displayed height of row in pixels */
- public int height = 0;
-
- public int graph = 0;
-
- public int graphHeight = 40;
-
- public boolean padGaps = false;
-
- public static final int NO_GRAPH = 0;
-
- public static final int BAR_GRAPH = 1;
-
- public static final int LINE_GRAPH = 2;
-
- public boolean belowAlignment = true;
-
- public SequenceGroup groupRef = null;
-
- /**
- * display every column label, even if there is a row of identical labels
- */
- public boolean showAllColLabels = false;
-
- /**
- * scale the column label to fit within the alignment column.
- */
- public boolean scaleColLabel = false;
-
- /**
- * centre the column labels relative to the alignment column
- */
- public boolean centreColLabels = false;
-
- private boolean isrna;
-
- public static int getGraphValueFromString(String string)
- {
- if (string.equalsIgnoreCase("BAR_GRAPH"))
- {
- return BAR_GRAPH;
- }
- else if (string.equalsIgnoreCase("LINE_GRAPH"))
- {
- return LINE_GRAPH;
- }
- else
- {
- return NO_GRAPH;
- }
- }
-
- /**
- * Creates a new AlignmentAnnotation object.
- *
- * @param label
- * short label shown under sequence labels
- * @param description
- * text displayed on mouseover
- * @param annotations
- * set of positional annotation elements
- */
- public AlignmentAnnotation(String label, String description,
- Annotation[] annotations)
- {
- setAnnotationId();
- // always editable?
- editable = true;
- this.label = label;
- this.description = description;
- this.annotations = annotations;
-
- validateRangeAndDisplay();
- }
-
- /**
- * Checks if annotation labels represent secondary structures
- *
- */
- void areLabelsSecondaryStructure()
- {
- boolean nonSSLabel = false;
- isrna = false;
- StringBuffer rnastring = new StringBuffer();
-
- char firstChar = 0;
- for (int i = 0; i < annotations.length; i++)
- {
- // DEBUG System.out.println(i + ": " + annotations[i]);
- if (annotations[i] == null)
- {
- continue;
- }
- if (annotations[i].secondaryStructure == 'H'
- || annotations[i].secondaryStructure == 'E')
- {
- // DEBUG System.out.println( "/H|E/ '" +
- // annotations[i].secondaryStructure + "'");
- hasIcons |= true;
- }
- else
- // Check for RNA secondary structure
- {
- // DEBUG System.out.println( "/else/ '" +
- // annotations[i].secondaryStructure + "'");
- // TODO: 2.8.2 should this ss symbol validation check be a function in
- // RNA/ResidueProperties ?
- if (annotations[i].secondaryStructure == '('
- || annotations[i].secondaryStructure == '['
- || annotations[i].secondaryStructure == '<'
- || annotations[i].secondaryStructure == '{'
- || annotations[i].secondaryStructure == 'A'
- || annotations[i].secondaryStructure == 'B'
- || annotations[i].secondaryStructure == 'C'
- || annotations[i].secondaryStructure == 'D'
- // || annotations[i].secondaryStructure == 'E' // ambiguous on
- // its own -- already checked above
- || annotations[i].secondaryStructure == 'F'
- || annotations[i].secondaryStructure == 'G'
- // || annotations[i].secondaryStructure == 'H' // ambiguous on
- // its own -- already checked above
- || annotations[i].secondaryStructure == 'I'
- || annotations[i].secondaryStructure == 'J'
- || annotations[i].secondaryStructure == 'K'
- || annotations[i].secondaryStructure == 'L'
- || annotations[i].secondaryStructure == 'M'
- || annotations[i].secondaryStructure == 'N'
- || annotations[i].secondaryStructure == 'O'
- || annotations[i].secondaryStructure == 'P'
- || annotations[i].secondaryStructure == 'Q'
- || annotations[i].secondaryStructure == 'R'
- || annotations[i].secondaryStructure == 'S'
- || annotations[i].secondaryStructure == 'T'
- || annotations[i].secondaryStructure == 'U'
- || annotations[i].secondaryStructure == 'V'
- || annotations[i].secondaryStructure == 'W'
- || annotations[i].secondaryStructure == 'X'
- || annotations[i].secondaryStructure == 'Y'
- || annotations[i].secondaryStructure == 'Z')
- {
- hasIcons |= true;
- isrna |= true;
- }
- }
-
- // System.out.println("displaychar " + annotations[i].displayCharacter);
-
- if (annotations[i].displayCharacter == null
- || annotations[i].displayCharacter.length() == 0)
- {
- rnastring.append('.');
- continue;
- }
- if (annotations[i].displayCharacter.length() == 1)
- {
- firstChar = annotations[i].displayCharacter.charAt(0);
- // check to see if it looks like a sequence or is secondary structure
- // labelling.
- if (annotations[i].secondaryStructure != ' ' && !hasIcons &&
- // Uncomment to only catch case where
- // displayCharacter==secondary
- // Structure
- // to correctly redisplay SS annotation imported from Stockholm,
- // exported to JalviewXML and read back in again.
- // &&
- // annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure
- firstChar != ' ' && firstChar != '$' && firstChar != 0xCE
- && firstChar != '(' && firstChar != '[' && firstChar != '<'
- && firstChar != '{' && firstChar != 'A' && firstChar != 'B'
- && firstChar != 'C' && firstChar != 'D' && firstChar != 'E'
- && firstChar != 'F' && firstChar != 'G' && firstChar != 'H'
- && firstChar != 'I' && firstChar != 'J' && firstChar != 'K'
- && firstChar != 'L' && firstChar != 'M' && firstChar != 'N'
- && firstChar != 'O' && firstChar != 'P' && firstChar != 'Q'
- && firstChar != 'R' && firstChar != 'S' && firstChar != 'T'
- && firstChar != 'U' && firstChar != 'V' && firstChar != 'W'
- && firstChar != 'X' && firstChar != 'Y' && firstChar != 'Z'
- && firstChar != '-'
- && firstChar < jalview.schemes.ResidueProperties.aaIndex.length)
- {
- if (jalview.schemes.ResidueProperties.aaIndex[firstChar] < 23) // TODO:
- // parameterise
- // to
- // gap
- // symbol
- // number
- {
- nonSSLabel = true;
- }
- }
- }
- else
- {
- rnastring.append(annotations[i].displayCharacter.charAt(1));
- }
-
- if (annotations[i].displayCharacter.length() > 0)
- {
- hasText = true;
- }
- }
-
- if (nonSSLabel)
- {
- hasIcons = false;
- for (int j = 0; j < annotations.length; j++)
- {
- if (annotations[j] != null
- && annotations[j].secondaryStructure != ' ')
- {
- annotations[j].displayCharacter = String
- .valueOf(annotations[j].secondaryStructure);
- annotations[j].secondaryStructure = ' ';
- }
-
- }
- }
- else
- {
- if (isrna)
- {
- _updateRnaSecStr(new AnnotCharSequence());
- }
- }
- }
-
- /**
- * flyweight access to positions in the alignment annotation row for RNA
- * processing
- *
- * @author jimp
- *
- */
- private class AnnotCharSequence implements CharSequence
- {
- int offset = 0;
-
- int max = 0;
-
- public AnnotCharSequence()
- {
- this(0, annotations.length);
- }
-
- AnnotCharSequence(int start, int end)
- {
- offset = start;
- max = end;
- }
-
- @Override
- public CharSequence subSequence(int start, int end)
- {
- return new AnnotCharSequence(offset + start, offset + end);
- }
-
- @Override
- public int length()
- {
- return max - offset;
- }
-
- @Override
- public char charAt(int index)
- {
- return ((index + offset < 0) || (index + offset) >= max
- || annotations[index + offset] == null
- || (annotations[index + offset].secondaryStructure <= ' ')
- ? ' '
- : annotations[index + offset].displayCharacter == null
- || annotations[index
- + offset].displayCharacter
- .length() == 0
- ? annotations[index
- + offset].secondaryStructure
- : annotations[index
- + offset].displayCharacter
- .charAt(0));
- }
-
- @Override
- public String toString()
- {
- char[] string = new char[max - offset];
- int mx = annotations.length;
-
- for (int i = offset; i < mx; i++)
- {
- string[i] = (annotations[i] == null
- || (annotations[i].secondaryStructure <= 32))
- ? ' '
- : (annotations[i].displayCharacter == null
- || annotations[i].displayCharacter
- .length() == 0
- ? annotations[i].secondaryStructure
- : annotations[i].displayCharacter
- .charAt(0));
- }
- return new String(string);
- }
- };
-
- private long _lastrnaannot = -1;
-
- public String getRNAStruc()
- {
- if (isrna)
- {
- String rnastruc = new AnnotCharSequence().toString();
- if (_lastrnaannot != rnastruc.hashCode())
- {
- // ensure rna structure contacts are up to date
- _lastrnaannot = rnastruc.hashCode();
- _updateRnaSecStr(rnastruc);
- }
- return rnastruc;
- }
- return null;
- }
-
- /**
- * Creates a new AlignmentAnnotation object.
- *
- * @param label
- * DOCUMENT ME!
- * @param description
- * DOCUMENT ME!
- * @param annotations
- * DOCUMENT ME!
- * @param min
- * DOCUMENT ME!
- * @param max
- * DOCUMENT ME!
- * @param winLength
- * DOCUMENT ME!
- */
- public AlignmentAnnotation(String label, String description,
- Annotation[] annotations, float min, float max, int graphType)
- {
- setAnnotationId();
- // graphs are not editable
- editable = graphType == 0;
-
- this.label = label;
- this.description = description;
- this.annotations = annotations;
- graph = graphType;
- graphMin = min;
- graphMax = max;
- validateRangeAndDisplay();
- }
-
- /**
- * checks graphMin and graphMax, secondary structure symbols, sets graphType
- * appropriately, sets null labels to the empty string if appropriate.
- */
- public void validateRangeAndDisplay()
- {
-
- if (annotations == null)
- {
- visible = false; // try to prevent renderer from displaying.
- invalidrnastruc = -1;
- return; // this is a non-annotation row annotation - ie a sequence score.
- }
-
- int graphType = graph;
- float min = graphMin;
- float max = graphMax;
- boolean drawValues = true;
- _linecolour = null;
- if (min == max)
- {
- min = 999999999;
- for (int i = 0; i < annotations.length; i++)
- {
- if (annotations[i] == null)
- {
- continue;
- }
-
- if (drawValues && annotations[i].displayCharacter != null
- && annotations[i].displayCharacter.length() > 1)
- {
- drawValues = false;
- }
-
- if (annotations[i].value > max)
- {
- max = annotations[i].value;
- }
-
- if (annotations[i].value < min)
- {
- min = annotations[i].value;
- }
- if (_linecolour == null && annotations[i].colour != null)
- {
- _linecolour = annotations[i].colour;
- }
- }
- // ensure zero is origin for min/max ranges on only one side of zero
- if (min > 0)
- {
- min = 0;
- }
- else
- {
- if (max < 0)
- {
- max = 0;
- }
- }
- }
-
- graphMin = min;
- graphMax = max;
-
- areLabelsSecondaryStructure();
-
- if (!drawValues && graphType != NO_GRAPH)
- {
- for (int i = 0; i < annotations.length; i++)
- {
- if (annotations[i] != null)
- {
- annotations[i].displayCharacter = "";
- }
- }
- }
- }
-
- /**
- * Copy constructor creates a new independent annotation row with the same
- * associated sequenceRef
- *
- * @param annotation
- */
- public AlignmentAnnotation(AlignmentAnnotation annotation)
- {
- setAnnotationId();
- this.label = new String(annotation.label);
- if (annotation.description != null)
- {
- this.description = new String(annotation.description);
- }
- this.graphMin = annotation.graphMin;
- this.graphMax = annotation.graphMax;
- this.graph = annotation.graph;
- this.graphHeight = annotation.graphHeight;
- this.graphGroup = annotation.graphGroup;
- this.groupRef = annotation.groupRef;
- this.editable = annotation.editable;
- this.autoCalculated = annotation.autoCalculated;
- this.hasIcons = annotation.hasIcons;
- this.hasText = annotation.hasText;
- this.height = annotation.height;
- this.label = annotation.label;
- this.padGaps = annotation.padGaps;
- this.visible = annotation.visible;
- this.centreColLabels = annotation.centreColLabels;
- this.scaleColLabel = annotation.scaleColLabel;
- this.showAllColLabels = annotation.showAllColLabels;
- this.calcId = annotation.calcId;
- if (annotation.properties != null)
- {
- properties = new HashMap<>();
- for (Map.Entry<String, String> val : annotation.properties.entrySet())
- {
- properties.put(val.getKey(), val.getValue());
- }
- }
- if (this.hasScore = annotation.hasScore)
- {
- this.score = annotation.score;
- }
- if (annotation.threshold != null)
- {
- threshold = new GraphLine(annotation.threshold);
- }
- Annotation[] ann = annotation.annotations;
- if (annotation.annotations != null)
- {
- this.annotations = new Annotation[ann.length];
- for (int i = 0; i < ann.length; i++)
- {
- if (ann[i] != null)
- {
- annotations[i] = new Annotation(ann[i]);
- if (_linecolour != null)
- {
- _linecolour = annotations[i].colour;
- }
- }
- }
- }
- if (annotation.sequenceRef != null)
- {
- this.sequenceRef = annotation.sequenceRef;
- if (annotation.sequenceMapping != null)
- {
- Integer p = null;
- sequenceMapping = new HashMap<>();
- Iterator<Integer> pos = annotation.sequenceMapping.keySet()
- .iterator();
- while (pos.hasNext())
- {
- // could optimise this!
- p = pos.next();
- Annotation a = annotation.sequenceMapping.get(p);
- if (a == null)
- {
- continue;
- }
- if (ann != null)
- {
- for (int i = 0; i < ann.length; i++)
- {
- if (ann[i] == a)
- {
- sequenceMapping.put(p, annotations[i]);
- }
- }
- }
- }
- }
- else
- {
- this.sequenceMapping = null;
- }
- }
- // TODO: check if we need to do this: JAL-952
- // if (this.isrna=annotation.isrna)
- {
- // _rnasecstr=new SequenceFeature[annotation._rnasecstr];
- }
- validateRangeAndDisplay(); // construct hashcodes, etc.
- }
-
- /**
- * clip the annotation to the columns given by startRes and endRes (inclusive)
- * and prune any existing sequenceMapping to just those columns.
- *
- * @param startRes
- * @param endRes
- */
- public void restrict(int startRes, int endRes)
- {
- if (annotations == null)
- {
- // non-positional
- return;
- }
- if (startRes < 0)
- {
- startRes = 0;
- }
- if (startRes >= annotations.length)
- {
- startRes = annotations.length - 1;
- }
- if (endRes >= annotations.length)
- {
- endRes = annotations.length - 1;
- }
- if (annotations == null)
- {
- return;
- }
- Annotation[] temp = new Annotation[endRes - startRes + 1];
- if (startRes < annotations.length)
- {
- System.arraycopy(annotations, startRes, temp, 0,
- endRes - startRes + 1);
- }
- if (sequenceRef != null)
- {
- // Clip the mapping, if it exists.
- int spos = sequenceRef.findPosition(startRes);
- int epos = sequenceRef.findPosition(endRes);
- if (sequenceMapping != null)
- {
- Map<Integer, Annotation> newmapping = new HashMap<>();
- Iterator<Integer> e = sequenceMapping.keySet().iterator();
- while (e.hasNext())
- {
- Integer pos = e.next();
- if (pos.intValue() >= spos && pos.intValue() <= epos)
- {
- newmapping.put(pos, sequenceMapping.get(pos));
- }
- }
- sequenceMapping.clear();
- sequenceMapping = newmapping;
- }
- }
- annotations = temp;
- }
-
- /**
- * set the annotation row to be at least length Annotations
- *
- * @param length
- * minimum number of columns required in the annotation row
- * @return false if the annotation row is greater than length
- */
- public boolean padAnnotation(int length)
- {
- if (annotations == null)
- {
- return true; // annotation row is correct - null == not visible and
- // undefined length
- }
- if (annotations.length < length)
- {
- Annotation[] na = new Annotation[length];
- System.arraycopy(annotations, 0, na, 0, annotations.length);
- annotations = na;
- return true;
- }
- return annotations.length > length;
-
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- @Override
- public String toString()
- {
- if (annotations == null)
- {
- return "";
- }
- StringBuilder buffer = new StringBuilder(256);
-
- for (int i = 0; i < annotations.length; i++)
- {
- if (annotations[i] != null)
- {
- if (graph != 0)
- {
- buffer.append(annotations[i].value);
- }
- else if (hasIcons)
- {
- buffer.append(annotations[i].secondaryStructure);
- }
- else
- {
- buffer.append(annotations[i].displayCharacter);
- }
- }
-
- buffer.append(", ");
- }
- // TODO: remove disgusting hack for 'special' treatment of consensus line.
- if (label.indexOf("Consensus") == 0)
- {
- buffer.append("\n");
-
- for (int i = 0; i < annotations.length; i++)
- {
- if (annotations[i] != null)
- {
- buffer.append(annotations[i].description);
- }
-
- buffer.append(", ");
- }
- }
-
- return buffer.toString();
- }
-
- public void setThreshold(GraphLine line)
- {
- threshold = line;
- }
-
- public GraphLine getThreshold()
- {
- return threshold;
- }
-
- /**
- * Attach the annotation to seqRef, starting from startRes position. If
- * alreadyMapped is true then the indices of the annotation[] array are
- * sequence positions rather than alignment column positions.
- *
- * @param seqRef
- * @param startRes
- * @param alreadyMapped
- */
- public void createSequenceMapping(SequenceI seqRef, int startRes,
- boolean alreadyMapped)
- {
-
- if (seqRef == null)
- {
- return;
- }
- sequenceRef = seqRef;
- if (annotations == null)
- {
- return;
- }
- sequenceMapping = new HashMap<>();
-
- int seqPos;
-
- for (int i = 0; i < annotations.length; i++)
- {
- if (annotations[i] != null)
- {
- if (alreadyMapped)
- {
- seqPos = seqRef.findPosition(i);
- }
- else
- {
- seqPos = i + startRes;
- }
-
- sequenceMapping.put(new Integer(seqPos), annotations[i]);
- }
- }
-
- }
-
- /**
- * When positional annotation and a sequence reference is present, clears and
- * resizes the annotations array to the current alignment width, and adds
- * annotation according to aligned positions of the sequenceRef given by
- * sequenceMapping.
- */
- public void adjustForAlignment()
- {
- if (sequenceRef == null)
- {
- return;
- }
-
- if (annotations == null)
- {
- return;
- }
-
- int a = 0, aSize = sequenceRef.getLength();
-
- if (aSize == 0)
- {
- // Its been deleted
- return;
- }
-
- int position;
- Annotation[] temp = new Annotation[aSize];
- Integer index;
- if (sequenceMapping != null)
- {
- for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++)
- {
- index = new Integer(a);
- Annotation annot = sequenceMapping.get(index);
- if (annot != null)
- {
- position = sequenceRef.findIndex(a) - 1;
-
- temp[position] = annot;
- }
- }
- }
- annotations = temp;
- }
-
- /**
- * remove any null entries in annotation row and return the number of non-null
- * annotation elements.
- *
- * @return
- */
- public int compactAnnotationArray()
- {
- int i = 0, iSize = annotations.length;
- while (i < iSize)
- {
- if (annotations[i] == null)
- {
- if (i + 1 < iSize)
- {
- System.arraycopy(annotations, i + 1, annotations, i,
- iSize - i - 1);
- }
- iSize--;
- }
- else
- {
- i++;
- }
- }
- Annotation[] ann = annotations;
- annotations = new Annotation[i];
- System.arraycopy(ann, 0, annotations, 0, i);
- ann = null;
- return iSize;
- }
-
- /**
- * Associate this annotation with the aligned residues of a particular
- * sequence. sequenceMapping will be updated in the following way: null
- * sequenceI - existing mapping will be discarded but annotations left in
- * mapped positions. valid sequenceI not equal to current sequenceRef: mapping
- * is discarded and rebuilt assuming 1:1 correspondence TODO: overload with
- * parameter to specify correspondence between current and new sequenceRef
- *
- * @param sequenceI
- */
- public void setSequenceRef(SequenceI sequenceI)
- {
- if (sequenceI != null)
- {
- if (sequenceRef != null)
- {
- boolean rIsDs = sequenceRef.getDatasetSequence() == null,
- tIsDs = sequenceI.getDatasetSequence() == null;
- if (sequenceRef != sequenceI
- && (rIsDs && !tIsDs
- && sequenceRef != sequenceI.getDatasetSequence())
- && (!rIsDs && tIsDs
- && sequenceRef.getDatasetSequence() != sequenceI)
- && (!rIsDs && !tIsDs
- && sequenceRef.getDatasetSequence() != sequenceI
- .getDatasetSequence())
- && !sequenceRef.equals(sequenceI))
- {
- // if sequenceRef isn't intersecting with sequenceI
- // throw away old mapping and reconstruct.
- sequenceRef = null;
- if (sequenceMapping != null)
- {
- sequenceMapping = null;
- // compactAnnotationArray();
- }
- createSequenceMapping(sequenceI, 1, true);
- adjustForAlignment();
- }
- else
- {
- // Mapping carried over
- sequenceRef = sequenceI;
- }
- }
- else
- {
- // No mapping exists
- createSequenceMapping(sequenceI, 1, true);
- adjustForAlignment();
- }
- }
- else
- {
- // throw away the mapping without compacting.
- sequenceMapping = null;
- sequenceRef = null;
- }
- }
-
- /**
- * @return the score
- */
- public double getScore()
- {
- return score;
- }
-
- /**
- * @param score
- * the score to set
- */
- public void setScore(double score)
- {
- hasScore = true;
- this.score = score;
- }
-
- /**
- *
- * @return true if annotation has an associated score
- */
- public boolean hasScore()
- {
- return hasScore || !Double.isNaN(score);
- }
-
- /**
- * Score only annotation
- *
- * @param label
- * @param description
- * @param score
- */
- public AlignmentAnnotation(String label, String description, double score)
- {
- this(label, description, null);
- setScore(score);
- }
-
- /**
- * copy constructor with edit based on the hidden columns marked in colSel
- *
- * @param alignmentAnnotation
- * @param colSel
- */
- public AlignmentAnnotation(AlignmentAnnotation alignmentAnnotation,
- HiddenColumns hidden)
- {
- this(alignmentAnnotation);
- if (annotations == null)
- {
- return;
- }
- makeVisibleAnnotation(hidden);
- }
-
- public void setPadGaps(boolean padgaps, char gapchar)
- {
- this.padGaps = padgaps;
- if (padgaps)
- {
- hasText = true;
- for (int i = 0; i < annotations.length; i++)
- {
- if (annotations[i] == null)
- {
- annotations[i] = new Annotation(String.valueOf(gapchar), null,
- ' ', 0f, null);
- }
- else if (annotations[i].displayCharacter == null
- || annotations[i].displayCharacter.equals(" "))
- {
- annotations[i].displayCharacter = String.valueOf(gapchar);
- }
- }
- }
- }
-
- /**
- * format description string for display
- *
- * @param seqname
- * @return Get the annotation description string optionally prefixed by
- * associated sequence name (if any)
- */
- public String getDescription(boolean seqname)
- {
- if (seqname && this.sequenceRef != null)
- {
- int i = description.toLowerCase().indexOf("<html>");
- if (i > -1)
- {
- // move the html tag to before the sequence reference.
- return "<html>" + sequenceRef.getName() + " : "
- + description.substring(i + 6);
- }
- return sequenceRef.getName() + " : " + description;
- }
- return description;
- }
-
- public boolean isValidStruc()
- {
- return invalidrnastruc == -1;
- }
-
- public long getInvalidStrucPos()
- {
- return invalidrnastruc;
- }
-
- /**
- * machine readable ID string indicating what generated this annotation
- */
- protected String calcId = "";
-
- /**
- * properties associated with the calcId
- */
- protected Map<String, String> properties = new HashMap<>();
-
- /**
- * base colour for line graphs. If null, will be set automatically by
- * searching the alignment annotation
- */
- public java.awt.Color _linecolour;
-
- public String getCalcId()
- {
- return calcId;
- }
-
- public void setCalcId(String calcId)
- {
- this.calcId = calcId;
- }
-
- public boolean isRNA()
- {
- return isrna;
- }
-
- /**
- * transfer annotation to the given sequence using the given mapping from the
- * current positions or an existing sequence mapping
- *
- * @param sq
- * @param sp2sq
- * map involving sq as To or From
- */
- public void liftOver(SequenceI sq, Mapping sp2sq)
- {
- if (sp2sq.getMappedWidth() != sp2sq.getWidth())
- {
- // TODO: employ getWord/MappedWord to transfer annotation between cDNA and
- // Protein reference frames
- throw new Error(
- "liftOver currently not implemented for transfer of annotation between different types of seqeunce");
- }
- boolean mapIsTo = (sp2sq != null)
- ? (sp2sq.getTo() == sq
- || sp2sq.getTo() == sq.getDatasetSequence())
- : false;
-
- // TODO build a better annotation element map and get rid of annotations[]
- Map<Integer, Annotation> mapForsq = new HashMap<>();
- if (sequenceMapping != null)
- {
- if (sp2sq != null)
- {
- int[] reg = new int[MapList.LEN];
- for (Entry<Integer, Annotation> ie : sequenceMapping.entrySet())
- {
- reg[MapList.POS] = ie.getKey();
- int mpos = sp2sq.getPosition(reg, mapIsTo);
- if (mpos >= sq.getStart() && mpos <= sq.getEnd())
- {
- mapForsq.put(mpos, ie.getValue());
- }
- }
- sequenceMapping = mapForsq;
- sequenceRef = sq;
- adjustForAlignment();
- }
- else
- {
- // trim positions
- }
- }
- }
-
- /**
- * like liftOver but more general.
- *
- * Takes an array of int pairs that will be used to update the internal
- * sequenceMapping and so shuffle the annotated positions
- *
- * @param newref
- * - new sequence reference for the annotation row - if null,
- * sequenceRef is left unchanged
- * @param mapping
- * array of ints containing corresponding positions
- * @param from
- * - column for current coordinate system (-1 for index+1)
- * @param to
- * - column for destination coordinate system (-1 for index+1)
- * @param idxoffset
- * - offset added to index when referencing either coordinate system
- * @note no checks are made as to whether from and/or to are sensible
- * @note caller should add the remapped annotation to newref if they have not
- * already
- */
- public void remap(SequenceI newref, HashMap<Integer, int[]> mapping,
- int from, int to, int idxoffset)
- {
- if (mapping != null)
- {
- Map<Integer, Annotation> old = sequenceMapping;
- Map<Integer, Annotation> remap = new HashMap<>();
- int index = -1;
- for (int mp[] : mapping.values())
- {
- if (index++ < 0)
- {
- continue;
- }
- Annotation ann = null;
- if (from == -1)
- {
- ann = sequenceMapping.get(Integer.valueOf(idxoffset + index));
- }
- else
- {
- if (mp != null && mp.length > from)
- {
- ann = sequenceMapping.get(Integer.valueOf(mp[from]));
- }
- }
- if (ann != null)
- {
- if (to == -1)
- {
- remap.put(Integer.valueOf(idxoffset + index), ann);
- }
- else
- {
- if (to > -1 && to < mp.length)
- {
- remap.put(Integer.valueOf(mp[to]), ann);
- }
- }
- }
- }
- sequenceMapping = remap;
- old.clear();
- if (newref != null)
- {
- sequenceRef = newref;
- }
- adjustForAlignment();
- }
- }
-
- public String getProperty(String property)
- {
- if (properties == null)
- {
- return null;
- }
- return properties.get(property);
- }
-
- public void setProperty(String property, String value)
- {
- if (properties == null)
- {
- properties = new HashMap<>();
- }
- properties.put(property, value);
- }
-
- public boolean hasProperties()
- {
- return properties != null && properties.size() > 0;
- }
-
- public Collection<String> getProperties()
- {
- if (properties == null)
- {
- return Collections.emptyList();
- }
- return properties.keySet();
- }
-
- /**
- * Returns the Annotation for the given sequence position (base 1) if any,
- * else null
- *
- * @param position
- * @return
- */
- public Annotation getAnnotationForPosition(int position)
- {
- return sequenceMapping == null ? null : sequenceMapping.get(position);
-
- }
-
- /**
- * Set the id to "ann" followed by a counter that increments so as to be
- * unique for the lifetime of the JVM
- */
- protected final void setAnnotationId()
- {
- this.annotationId = ANNOTATION_ID_PREFIX + Long.toString(nextId());
- }
-
- /**
- * Returns the match for the last unmatched opening RNA helix pair symbol
- * preceding the given column, or '(' if nothing found to match.
- *
- * @param column
- * @return
- */
- public String getDefaultRnaHelixSymbol(int column)
- {
- String result = "(";
- if (annotations == null)
- {
- return result;
- }
-
- /*
- * for each preceding column, if it contains an open bracket,
- * count whether it is still unmatched at column, if so return its pair
- * (likely faster than the fancy alternative using stacks)
- */
- for (int col = column - 1; col >= 0; col--)
- {
- Annotation annotation = annotations[col];
- if (annotation == null)
- {
- continue;
- }
- String displayed = annotation.displayCharacter;
- if (displayed == null || displayed.length() != 1)
- {
- continue;
- }
- char symbol = displayed.charAt(0);
- if (!Rna.isOpeningParenthesis(symbol))
- {
- continue;
- }
-
- /*
- * found an opening bracket symbol
- * count (closing-opening) symbols of this type that follow it,
- * up to and excluding the target column; if the count is less
- * than 1, the opening bracket is unmatched, so return its match
- */
- String closer = String
- .valueOf(Rna.getMatchingClosingParenthesis(symbol));
- String opener = String.valueOf(symbol);
- int count = 0;
- for (int j = col + 1; j < column; j++)
- {
- if (annotations[j] != null)
- {
- String s = annotations[j].displayCharacter;
- if (closer.equals(s))
- {
- count++;
- }
- else if (opener.equals(s))
- {
- count--;
- }
- }
- }
- if (count < 1)
- {
- return closer;
- }
- }
- return result;
- }
-
- protected static synchronized long nextId()
- {
- return counter++;
- }
-
- /**
- *
- * @return true for rows that have a range of values in their annotation set
- */
- public boolean isQuantitative()
- {
- return graphMin < graphMax;
- }
-
- /**
- * delete any columns in alignmentAnnotation that are hidden (including
- * sequence associated annotation).
- *
- * @param hiddenColumns
- * the set of hidden columns
- */
- public void makeVisibleAnnotation(HiddenColumns hiddenColumns)
- {
- if (annotations != null)
- {
- makeVisibleAnnotation(0, annotations.length, hiddenColumns);
- }
- }
-
- /**
- * delete any columns in alignmentAnnotation that are hidden (including
- * sequence associated annotation).
- *
- * @param start
- * remove any annotation to the right of this column
- * @param end
- * remove any annotation to the left of this column
- * @param hiddenColumns
- * the set of hidden columns
- */
- public void makeVisibleAnnotation(int start, int end,
- HiddenColumns hiddenColumns)
- {
- if (annotations != null)
- {
- if (hiddenColumns.hasHiddenColumns())
- {
- removeHiddenAnnotation(start, end, hiddenColumns);
- }
- else
- {
- restrict(start, end);
- }
- }
- }
-
- /**
- * The actual implementation of deleting hidden annotation columns
- *
- * @param start
- * remove any annotation to the right of this column
- * @param end
- * remove any annotation to the left of this column
- * @param hiddenColumns
- * the set of hidden columns
- */
- private void removeHiddenAnnotation(int start, int end,
- HiddenColumns hiddenColumns)
- {
- // mangle the alignmentAnnotation annotation array
- ArrayList<Annotation[]> annels = new ArrayList<>();
- Annotation[] els = null;
-
- int w = 0;
-
- Iterator<int[]> blocks = hiddenColumns.getVisContigsIterator(start,
- end + 1, false);
-
- int copylength;
- int annotationLength;
- while (blocks.hasNext())
- {
- int[] block = blocks.next();
- annotationLength = block[1] - block[0] + 1;
-
- if (blocks.hasNext())
- {
- // copy just the visible segment of the annotation row
- copylength = annotationLength;
- }
- else
- {
- if (annotationLength + block[0] <= annotations.length)
- {
- // copy just the visible segment of the annotation row
- copylength = annotationLength;
- }
- else
- {
- // copy to the end of the annotation row
- copylength = annotations.length - block[0];
- }
- }
-
- els = new Annotation[annotationLength];
- annels.add(els);
- System.arraycopy(annotations, block[0], els, 0, copylength);
- w += annotationLength;
- }
-
- if (w != 0)
- {
- annotations = new Annotation[w];
-
- w = 0;
- for (Annotation[] chnk : annels)
- {
- System.arraycopy(chnk, 0, annotations, w, chnk.length);
- w += chnk.length;
- }
- }
- }
-
- public static Iterable<AlignmentAnnotation> findAnnotations(
- Iterable<AlignmentAnnotation> list, SequenceI seq, String calcId,
- String label)
- {
-
- ArrayList<AlignmentAnnotation> aa = new ArrayList<>();
- for (AlignmentAnnotation ann : list)
- {
- if ((calcId == null || (ann.getCalcId() != null
- && ann.getCalcId().equals(calcId)))
- && (seq == null || (ann.sequenceRef != null
- && ann.sequenceRef == seq))
- && (label == null
- || (ann.label != null && ann.label.equals(label))))
- {
- aa.add(ann);
- }
- }
- return aa;
- }
-
- /**
- * Answer true if any annotation matches the calcId passed in (if not null).
- *
- * @param list
- * annotation to search
- * @param calcId
- * @return
- */
- public static boolean hasAnnotation(List<AlignmentAnnotation> list,
- String calcId)
- {
-
- if (calcId != null && !"".equals(calcId))
- {
- for (AlignmentAnnotation a : list)
- {
- if (a.getCalcId() == calcId)
- {
- return true;
- }
- }
- }
- return false;
- }
-
- public static Iterable<AlignmentAnnotation> findAnnotation(
- List<AlignmentAnnotation> list, String calcId)
- {
-
- List<AlignmentAnnotation> aa = new ArrayList<>();
- if (calcId == null)
- {
- return aa;
- }
- for (AlignmentAnnotation a : list)
- {
-
- if (a.getCalcId() == calcId || (a.getCalcId() != null
- && calcId != null && a.getCalcId().equals(calcId)))
- {
- aa.add(a);
- }
- }
- return aa;
- }
-
-}
git://source.jalview.org / jalview.git / blobdiff