X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=483c82177bf07915e3eba54dd845b5f65d3e681a;hb=aaace4c8c53d4bb08a5bad0ea18ccfedbef90cd9;hp=d8ad4fc1a0e4b9ab357bae5531db4c6ecfdbd25e;hpb=d4c1851efd67ba892144ec32004c67701e72ce08;p=jalview.git diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java index d8ad4fc..483c821 100755 --- a/src/jalview/datamodel/AlignmentAnnotation.java +++ b/src/jalview/datamodel/AlignmentAnnotation.java @@ -1,20 +1,19 @@ /* - * 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 2.6) + * Copyright (C) 2010 J Procter, AM Waterhouse, 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; @@ -70,21 +69,21 @@ 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; @@ -101,13 +100,13 @@ public class AlignmentAnnotation public boolean belowAlignment = true; - public SequenceGroup groupRef =null ; + public SequenceGroup groupRef = null; /** * display every column label, even if there is a row of identical labels */ - public boolean showAllColLabels=false; - + public boolean showAllColLabels = false; + /** * scale the column label to fit within the alignment column. */ @@ -118,12 +117,14 @@ public class AlignmentAnnotation */ public boolean centreColLabels = false; - - /* (non-Javadoc) + /* + * (non-Javadoc) + * * @see java.lang.Object#finalize() */ protected void finalize() throws Throwable { + sequenceRef = null; groupRef = null; super.finalize(); } @@ -148,11 +149,11 @@ 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) @@ -179,7 +180,7 @@ public class AlignmentAnnotation if (annotations[i].secondaryStructure == 'H' || annotations[i].secondaryStructure == 'E') { - hasIcons = true; + hasIcons |= true; } if (annotations[i].displayCharacter == null) @@ -191,19 +192,28 @@ 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 < 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; } @@ -239,17 +249,17 @@ public class AlignmentAnnotation * 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) @@ -310,6 +320,18 @@ 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; @@ -358,7 +380,7 @@ public class AlignmentAnnotation { this.score = annotation.score; } - if (threshold != null) + if (annotation.threshold != null) { threshold = new GraphLine(annotation.threshold); } @@ -462,7 +484,7 @@ 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) @@ -470,7 +492,7 @@ public class AlignmentAnnotation if (annotations == null) { return true; // annotation row is correct - null == not visible and - // undefined length + // undefined length } if (annotations.length < length) { @@ -513,7 +535,7 @@ public class AlignmentAnnotation buffer.append(", "); } // TODO: remove disgusting hack for 'special' treatment of consensus line. - if (label.indexOf("Consensus")==0) + if (label.indexOf("Consensus") == 0) { buffer.append("\n"); @@ -715,7 +737,7 @@ public class AlignmentAnnotation /** * @param score - * the score to set + * the score to set */ public void setScore(double score) { @@ -791,6 +813,12 @@ 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;