X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=1d624d4adf16d2b94da968b2ca9b8b3c2b1ca032;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=d75683c60e6833ee58dd22613b2a96b099593619;hpb=133454102814512287d6bb5b1f4e5c2601eea863;p=jalview.git diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java index d75683c..1d624d4 100755 --- a/src/jalview/datamodel/AlignmentAnnotation.java +++ b/src/jalview/datamodel/AlignmentAnnotation.java @@ -1,307 +1,826 @@ -/* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle -* -* This program 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 2 -* of the License, or (at your option) any later version. -* -* This program 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 this program; if not, write to the Free Software -* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA -*/ -package jalview.datamodel; - - -/** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ -public class AlignmentAnnotation -{ - public SequenceI sequenceRef; - - /** DOCUMENT ME!! */ - public String label; - - /** DOCUMENT ME!! */ - public String description; - - /** DOCUMENT ME!! */ - public Annotation[] annotations; - - public java.util.Hashtable sequenceMapping; - - /** DOCUMENT ME!! */ - public float graphMin; - - /** DOCUMENT ME!! */ - public float graphMax; - - public GraphLine threshold; - - // Graphical hints and tips - - /** DOCUMENT ME!! */ - public boolean editable = false; - - /** DOCUMENT ME!! */ - public boolean hasIcons; // - - /** DOCUMENT ME!! */ - public boolean hasText; - - /** DOCUMENT ME!! */ - public boolean visible = true; - - public int graphGroup = -1; - - /** DOCUMENT ME!! */ - public int height = 0; - - public int graph = 0; - - public int graphHeight = 40; - - public static final int NO_GRAPH = 0; - - public static final int BAR_GRAPH = 1; - - public static final int LINE_GRAPH = 2; - - 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 DOCUMENT ME! - * @param description DOCUMENT ME! - * @param annotations DOCUMENT ME! - */ - public AlignmentAnnotation(String label, String description, - Annotation[] annotations) - { - // always editable? - editable = true; - this.label = label; - this.description = description; - this.annotations = annotations; - - for (int i = 0; i < annotations.length; i++) - { - if ((annotations[i] != null) && - ((annotations[i].secondaryStructure == 'H') || - (annotations[i].secondaryStructure == 'E'))) - { - hasIcons = true; - } - - if ((annotations[i] != null) && - (annotations[i].displayCharacter.length() > 0)) - { - hasText = true; - } - } - } - - /** - * 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) - { - // graphs are not editable - this.label = label; - this.description = description; - this.annotations = annotations; - graph = graphType; - - if (min == max) - { - min = 999999999; - for (int i = 0; i < annotations.length; i++) - { - if (annotations[i] == null) - { - continue; - } - - if (annotations[i].value > max) - { - max = annotations[i].value; - } - - if (annotations[i].value < min) - { - min = annotations[i].value; - } - } - } - - graphMin = min; - graphMax = max; - - for (int i = 0; i < annotations.length; i++) - { - if ((annotations[i] != null) && - ((annotations[i].secondaryStructure == 'H') || - (annotations[i].secondaryStructure == 'E'))) - { - hasIcons = true; - } - - if ((annotations[i] != null) && - (annotations[i].displayCharacter.length() > 0)) - { - hasText = true; - } - } - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public String toString() - { - StringBuffer buffer = new StringBuffer(); - - 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(", "); - } - - if (label.equals("Consensus")) - { - 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; - } - - /** - * This - */ - public void createSequenceMapping(SequenceI seqRef, int startRes) - { - if(seqRef == null) - return; - - sequenceMapping = new java.util.Hashtable(); - - sequenceRef = seqRef; - - if(startRes < sequenceRef.getStart()) - startRes = sequenceRef.getStart(); - - int seqPos, seqIndex; - - int fileOffset = 0; - if(startRes > sequenceRef.getStart()) - { - fileOffset = startRes - sequenceRef.getStart(); - } - - for(int i = 0; i < annotations.length; i++) - { - seqPos = sequenceRef.findPosition(i - fileOffset)-1; - if(seqPos=startRes) - sequenceMapping.put(new Integer(seqIndex), - annotations[seqPos]); - } - } - } - - adjustForAlignment(); - - } - - public void adjustForAlignment() - { - int a=0, aSize = sequenceRef.getLength(); - - int position; - Annotation[] temp = new Annotation[aSize]; - Integer index; - for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++) - { - index = new Integer(a); - if(sequenceMapping.containsKey(index)) - { - position = sequenceRef.findIndex(a)-1; - - temp[position] = (Annotation)sequenceMapping.get(index); - } - } - - annotations = temp; - } -} - - +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * + * 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 . + */ +package jalview.datamodel; + +import java.util.Enumeration; +import java.util.Hashtable; + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class AlignmentAnnotation +{ + /** + * If true, this annotations is calculated every edit, eg consensus, quality + * or conservation graphs + */ + public boolean autoCalculated = false; + + public String annotationId; + + public SequenceI sequenceRef; + + /** DOCUMENT ME!! */ + public String label; + + /** DOCUMENT ME!! */ + public String description; + + /** DOCUMENT ME!! */ + public Annotation[] annotations; + + public java.util.Hashtable sequenceMapping; + + /** DOCUMENT ME!! */ + public float graphMin; + + /** DOCUMENT ME!! */ + 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; + + /* + * (non-Javadoc) + * + * @see java.lang.Object#finalize() + */ + protected void finalize() throws Throwable + { + sequenceRef = null; + groupRef = null; + super.finalize(); + } + + 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) + { + // always editable? + editable = true; + this.label = label; + this.description = description; + this.annotations = annotations; + + validateRangeAndDisplay(); + } + + void areLabelsSecondaryStructure() + { + boolean nonSSLabel = false; + char firstChar = 0; + for (int i = 0; i < annotations.length; i++) + { + if (annotations[i] == null) + { + continue; + } + if (annotations[i].secondaryStructure == 'H' + || annotations[i].secondaryStructure == 'E') + { + hasIcons |= true; + } + + if (annotations[i].displayCharacter == null) + { + 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 != 'H' + && firstChar != 'E' + && firstChar != '-' + && firstChar < jalview.schemes.ResidueProperties.aaIndex.length) + { + if (jalview.schemes.ResidueProperties.aaIndex[firstChar] < 23) // TODO: + // parameterise + // to + // gap + // symbol + // number + { + nonSSLabel = true; + } + } + } + + 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 = ' '; + } + + } + } + + annotationId = this.hashCode() + ""; + } + + /** + * 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) + { + // 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. + */ + private void validateRangeAndDisplay() + { + + if (annotations == null) + { + visible = false; // try to prevent renderer from displaying. + return; // this is a non-annotation row annotation - ie a sequence score. + } + + int graphType = graph; + float min = graphMin; + float max = graphMax; + boolean drawValues = true; + + 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; + } + } + // 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) + { + 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; + if (this.hasScore = annotation.hasScore) + { + this.score = annotation.score; + } + if (annotation.threshold != null) + { + threshold = new GraphLine(annotation.threshold); + } + if (annotation.annotations != null) + { + Annotation[] ann = annotation.annotations; + this.annotations = new Annotation[ann.length]; + for (int i = 0; i < ann.length; i++) + { + annotations[i] = new Annotation(ann[i]); + } + ; + if (annotation.sequenceRef != null) + { + this.sequenceRef = annotation.sequenceRef; + if (annotation.sequenceMapping != null) + { + Integer p = null; + sequenceMapping = new Hashtable(); + Enumeration pos = annotation.sequenceMapping.keys(); + while (pos.hasMoreElements()) + { + // could optimise this! + p = (Integer) pos.nextElement(); + Annotation a = (Annotation) annotation.sequenceMapping.get(p); + if (a == null) + { + continue; + } + for (int i = 0; i < ann.length; i++) + { + if (ann[i] == a) + { + sequenceMapping.put(p, annotations[i]); + } + } + } + } + else + { + this.sequenceMapping = null; + } + } + } + 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) + { + Hashtable newmapping = new Hashtable(); + Enumeration e = sequenceMapping.keys(); + while (e.hasMoreElements()) + { + Integer pos = (Integer) e.nextElement(); + 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! + */ + public String toString() + { + StringBuffer buffer = new StringBuffer(); + + 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 java.util.Hashtable(); + + 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]); + } + } + + } + + 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; + + for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++) + { + index = new Integer(a); + if (sequenceMapping.containsKey(index)) + { + position = sequenceRef.findIndex(a) - 1; + + temp[position] = (Annotation) sequenceMapping.get(index); + } + } + + 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 annotion 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) + { + if (sequenceRef != sequenceI + && !sequenceRef.equals(sequenceI) + && sequenceRef.getDatasetSequence() != sequenceI + .getDatasetSequence()) + { + // 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, + ColumnSelection colSel) + { + this(alignmentAnnotation); + if (annotations == null) + { + return; + } + colSel.makeVisibleAnnotation(this); + } + + 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); + 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; + } +}