X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;fp=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=470497e12ceff0a258443205d43fa153667df87b;hb=e894eb87d40be6e8452d19032ddffe80dad5f804;hp=c3ccb0ba99b0eba2867bdc5ec17bf02a2e84eb07;hpb=0f71bfca98457c30f1051f142c31b6aaa3e23ead;p=jalview.git diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java index c3ccb0b..470497e 100755 --- a/src/jalview/datamodel/AlignmentAnnotation.java +++ b/src/jalview/datamodel/AlignmentAnnotation.java @@ -1,267 +1,322 @@ -/* -* 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; - - /** This annotation is the original loaded annotation - * without any gaps. It is necessary to adjust the annotation - * if sequences are updated */ - public AlignmentAnnotation datasetAnnotation; - - /** DOCUMENT ME!! */ - public String label; - - /** DOCUMENT ME!! */ - public String description; - - /** DOCUMENT ME!! */ - public Annotation[] annotations; - - - /** 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; - } - - public void adjustForAlignment() - { - int a=0, aSize = sequenceRef.getLength(); - - int index = 0; - Annotation[] temp = new Annotation[aSize]; - - for (a = 0; a < aSize; a++) - { - if (!jalview.util.Comparison.isGap(sequenceRef.getCharAt(a))) - { - index = sequenceRef.findPosition(a); - if(datasetAnnotation.annotations.length>index) - temp[a] = datasetAnnotation.annotations[index]; - } - } - - annotations = temp; - } -} - - +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2006 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; + + 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.length() > 1 ) + { + drawValues = false; + } + + 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 (!hasIcons + && annotations[i] != null + && ((annotations[i].secondaryStructure == 'H') || + (annotations[i].secondaryStructure == 'E'))) + { + hasIcons = true; + } + + if (!hasText + && annotations[i]!=null + && annotations[i].displayCharacter.length() > 0) + { + hasText = true; + } + } + + if(!drawValues && graphType!=NO_GRAPH) + { + for (int i = 0; i < annotations.length; i++) + { + if (annotations[i] != null) + annotations[i].displayCharacter = ""; + } + } + } + + /** + * 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; + } + + /** + * Attach the annotation to seqRef, starting from startRes position. + * @param seqRef + * @param startRes + */ + public void createSequenceMapping(SequenceI seqRef, + int startRes, + boolean alreadyMapped) + { + if(seqRef == null) + return; + + sequenceMapping = new java.util.Hashtable(); + + sequenceRef = seqRef; + 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]); + } + } + + adjustForAlignment(); + } + + public void adjustForAlignment() + { + 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; + } +} + +