X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=25bba51748693aa0fe86fd55880e25e7609190cd;hb=34286266321abbbab6d462c39f500650f9c860c9;hp=adc25c2165c7eb4df19325df3a47e7cb1580360a;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java index adc25c2..25bba51 100755 --- a/src/jalview/datamodel/AlignmentAnnotation.java +++ b/src/jalview/datamodel/AlignmentAnnotation.java @@ -1,23 +1,24 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) - * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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 file is part of Jalview. * - * 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. + * 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. * - * 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 + * 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 jalview.analysis.Rna; + import java.util.Enumeration; import java.util.Hashtable; @@ -36,7 +37,7 @@ public class AlignmentAnnotation public boolean autoCalculated = false; public String annotationId; - + public SequenceI sequenceRef; /** DOCUMENT ME!! */ @@ -48,6 +49,35 @@ public class AlignmentAnnotation /** DOCUMENT ME!! */ public Annotation[] annotations; + /** + * RNA secondary structure contact positions + */ + public SequenceFeature[] _rnasecstr = null; + + public String rnaStructure; + + /** + * Updates the _rnasecstr field Determines the positions that base pair and + * the positions of helices based on secondary structure from a Stockholm file + * + * @param RNAannot + */ + private void _updateRnaSecStr(String RNAannot) + { + _rnasecstr = Rna.GetBasePairs(RNAannot); + Rna.HelixMap(_rnasecstr); + + setRNAStruc(RNAannot); + + if (_rnasecstr != null && _rnasecstr.length > 0) + { + // show all the RNA secondary structure annotation symbols. + showAllColLabels = true; + scaleColLabel = true; + } + // System.out.println("featuregroup " + _rnasecstr[0].getFeatureGroup()); + } + public java.util.Hashtable sequenceMapping; /** DOCUMENT ME!! */ @@ -70,21 +100,21 @@ public class AlignmentAnnotation // Graphical hints and tips - /** DOCUMENT ME!! */ + /** Can this row be edited by the user ? */ public boolean editable = false; - /** DOCUMENT ME!! */ + /** Indicates if annotation has a graphical symbol track */ public boolean hasIcons; // - /** DOCUMENT ME!! */ + /** Indicates if annotation has a text character label */ public boolean hasText; - /** DOCUMENT ME!! */ + /** is the row visible */ public boolean visible = true; public int graphGroup = -1; - /** DOCUMENT ME!! */ + /** Displayed height of row in pixels */ public int height = 0; public int graph = 0; @@ -101,6 +131,35 @@ public class AlignmentAnnotation 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")) @@ -121,11 +180,11 @@ public class AlignmentAnnotation * Creates a new AlignmentAnnotation object. * * @param label - * short label shown under sequence labels + * short label shown under sequence labels * @param description - * text displayed on mouseover + * text displayed on mouseover * @param annotations - * set of positional annotation elements + * set of positional annotation elements */ public AlignmentAnnotation(String label, String description, Annotation[] annotations) @@ -139,9 +198,16 @@ public class AlignmentAnnotation validateRangeAndDisplay(); } + /** + * Checks if annotation labels represent secondary structures + * + */ void areLabelsSecondaryStructure() { boolean nonSSLabel = false; + boolean isrna = false; + StringBuffer rnastring = new StringBuffer(); + char firstChar = 0; for (int i = 0; i < annotations.length; i++) { @@ -152,11 +218,24 @@ public class AlignmentAnnotation if (annotations[i].secondaryStructure == 'H' || annotations[i].secondaryStructure == 'E') { - hasIcons = true; + hasIcons |= true; + } + else + // Check for RNA secondary structure + { + if (annotations[i].secondaryStructure == 'S') + { + hasIcons |= true; + isrna |= true; + } } - if (annotations[i].displayCharacter == null) + // 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) @@ -164,25 +243,38 @@ public class AlignmentAnnotation firstChar = annotations[i].displayCharacter.charAt(0); // check to see if it looks like a sequence or is secondary structure // labelling. - if ( - // 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 != 'H' + 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 != 'S' && firstChar != '-' && firstChar < jalview.schemes.ResidueProperties.aaIndex.length) { - if (jalview.schemes.ResidueProperties.aaIndex[firstChar] < 23) + 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) { @@ -205,25 +297,40 @@ public class AlignmentAnnotation } } + else + { + if (isrna) + { + _updateRnaSecStr(rnastring.toString()); + } + } annotationId = this.hashCode() + ""; } - /** + public void setRNAStruc(String string) { + rnaStructure=string; +} + + public String getRNAStruc(){ + return rnaStructure; + } + +/** * Creates a new AlignmentAnnotation object. * * @param label - * DOCUMENT ME! + * DOCUMENT ME! * @param description - * DOCUMENT ME! + * DOCUMENT ME! * @param annotations - * DOCUMENT ME! + * DOCUMENT ME! * @param min - * DOCUMENT ME! + * DOCUMENT ME! * @param max - * DOCUMENT ME! + * DOCUMENT ME! * @param winLength - * DOCUMENT ME! + * DOCUMENT ME! */ public AlignmentAnnotation(String label, String description, Annotation[] annotations, float min, float max, int graphType) @@ -244,7 +351,7 @@ public class AlignmentAnnotation * checks graphMin and graphMax, secondary structure symbols, sets graphType * appropriately, sets null labels to the empty string if appropriate. */ - private void validateRangeAndDisplay() + public void validateRangeAndDisplay() { if (annotations == null) @@ -284,6 +391,18 @@ public class AlignmentAnnotation 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; @@ -319,6 +438,7 @@ public class AlignmentAnnotation 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; @@ -331,7 +451,7 @@ public class AlignmentAnnotation { this.score = annotation.score; } - if (threshold != null) + if (annotation.threshold != null) { threshold = new GraphLine(annotation.threshold); } @@ -435,7 +555,7 @@ public class AlignmentAnnotation * set the annotation row to be at least length Annotations * * @param length - * minimum number of columns required in the annotation row + * minimum number of columns required in the annotation row * @return false if the annotation row is greater than length */ public boolean padAnnotation(int length) @@ -443,7 +563,7 @@ public class AlignmentAnnotation if (annotations == null) { return true; // annotation row is correct - null == not visible and - // undefined length + // undefined length } if (annotations.length < length) { @@ -485,8 +605,8 @@ public class AlignmentAnnotation buffer.append(", "); } - - if (label.equals("Consensus")) + // TODO: remove disgusting hack for 'special' treatment of consensus line. + if (label.indexOf("Consensus") == 0) { buffer.append("\n"); @@ -688,7 +808,7 @@ public class AlignmentAnnotation /** * @param score - * the score to set + * the score to set */ public void setScore(double score) { @@ -764,6 +884,12 @@ public class AlignmentAnnotation { 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;