X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=unused%2FAlignmentAnnotation.java;fp=unused%2FAlignmentAnnotation.java;h=e9ca0c4468dc6b8a6e381ba663312699d572a48d;hb=ec8f3cedf60fb1feed6d34de6b49f6bfa78b9dd8;hp=0000000000000000000000000000000000000000;hpb=056dad85a910551cc95e44d451a61f6b8c4dd35d;p=jalview.git
diff --git a/unused/AlignmentAnnotation.java b/unused/AlignmentAnnotation.java
new file mode 100644
index 0000000..e9ca0c4
--- /dev/null
+++ b/unused/AlignmentAnnotation.java
@@ -0,0 +1,1718 @@
+/*
+ * 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 .
+ * 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 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 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 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 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 newmapping = new HashMap<>();
+ Iterator 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("");
+ if (i > -1)
+ {
+ // move the html tag to before the sequence reference.
+ return "" + 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 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 mapForsq = new HashMap<>();
+ if (sequenceMapping != null)
+ {
+ if (sp2sq != null)
+ {
+ int[] reg = new int[MapList.LEN];
+ for (Entry 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 mapping,
+ int from, int to, int idxoffset)
+ {
+ if (mapping != null)
+ {
+ Map old = sequenceMapping;
+ Map 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 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 annels = new ArrayList<>();
+ Annotation[] els = null;
+
+ int w = 0;
+
+ Iterator 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 findAnnotations(
+ Iterable list, SequenceI seq, String calcId,
+ String label)
+ {
+
+ ArrayList 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 list,
+ String calcId)
+ {
+
+ if (calcId != null && !"".equals(calcId))
+ {
+ for (AlignmentAnnotation a : list)
+ {
+ if (a.getCalcId() == calcId)
+ {
+ return true;
+ }
+ }
+ }
+ return false;
+ }
+
+ public static Iterable findAnnotation(
+ List list, String calcId)
+ {
+
+ List 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;
+ }
+
+}