X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=5d97fe3bd3759235e7ad84571297bc079157e568;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=6c119364fb62b9b77b531696e54f9a54e718960c;hpb=f52f7b378972cc884b5d3e5cc250f89667f558f7;p=jalview.git diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java index 6c11936..5d97fe3 100755 --- a/src/jalview/datamodel/Alignment.java +++ b/src/jalview/datamodel/Alignment.java @@ -1,19 +1,20 @@ /* - * 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 - * + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1) + * Copyright (C) 2014 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 + * 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 + * + * 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; @@ -24,7 +25,7 @@ import java.util.*; */ /** * @author JimP - * + * */ public class Alignment implements AlignmentI { @@ -77,7 +78,7 @@ public class Alignment implements AlignmentI /** * Make an alignment from an array of Sequences. - * + * * @param sequences */ public Alignment(SequenceI[] seqs) @@ -87,7 +88,7 @@ public class Alignment implements AlignmentI /** * Make a new alignment from an array of SeqCigars - * + * * @param seqs * SeqCigar[] */ @@ -103,7 +104,7 @@ public class Alignment implements AlignmentI * compactAlignment does not contain hidden regions. JBPNote - must also check * that compactAlignment resolves to a set of SeqCigars - or construct them * appropriately. - * + * * @param compactAlignment * CigarArray */ @@ -115,7 +116,7 @@ public class Alignment implements AlignmentI /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ @Override @@ -146,10 +147,10 @@ public class Alignment implements AlignmentI /** * DOCUMENT ME! - * + * * @param i * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ @Override @@ -167,7 +168,7 @@ public class Alignment implements AlignmentI /** * Adds a sequence to the alignment. Recalculates maxLength and size. - * + * * @param snew */ @Override @@ -206,7 +207,7 @@ public class Alignment implements AlignmentI /** * Adds a sequence to the alignment. Recalculates maxLength and size. - * + * * @param snew */ @Override @@ -222,7 +223,7 @@ public class Alignment implements AlignmentI /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ @Override @@ -258,7 +259,7 @@ public class Alignment implements AlignmentI /** * DOCUMENT ME! - * + * * @param s * DOCUMENT ME! */ @@ -270,7 +271,7 @@ public class Alignment implements AlignmentI /** * DOCUMENT ME! - * + * * @param i * DOCUMENT ME! */ @@ -289,7 +290,7 @@ public class Alignment implements AlignmentI /* * (non-Javadoc) - * + * * @see jalview.datamodel.AlignmentI#findGroup(jalview.datamodel.SequenceI) */ @Override @@ -312,7 +313,7 @@ public class Alignment implements AlignmentI /* * (non-Javadoc) - * + * * @see * jalview.datamodel.AlignmentI#findAllGroups(jalview.datamodel.SequenceI) */ @@ -370,7 +371,7 @@ public class Alignment implements AlignmentI return; } } - + sg.setContext(this); groups.add(sg); } } @@ -378,7 +379,7 @@ public class Alignment implements AlignmentI /** * remove any annotation that references gp - * + * * @param gp * (if null, removes all group associated annotation) */ @@ -445,6 +446,9 @@ public class Alignment implements AlignmentI { removeAnnotationForGroup(null); } + for (SequenceGroup sg:groups) { + sg.setContext(null); + } groups.clear(); } } @@ -459,6 +463,7 @@ public class Alignment implements AlignmentI { removeAnnotationForGroup(g); groups.remove(g); + g.setContext(null); } } } @@ -472,7 +477,7 @@ public class Alignment implements AlignmentI /* * (non-Javadoc) - * + * * @see jalview.datamodel.AlignmentI#findName(java.lang.String, boolean) */ @Override @@ -483,7 +488,7 @@ public class Alignment implements AlignmentI /* * (non-Javadoc) - * + * * @see jalview.datamodel.AlignmentI#findName(SequenceI, java.lang.String, * boolean) */ @@ -555,7 +560,7 @@ public class Alignment implements AlignmentI /* * (non-Javadoc) - * + * * @see jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SequenceI) */ @Override @@ -578,7 +583,7 @@ public class Alignment implements AlignmentI /* * (non-Javadoc) - * + * * @see * jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults) */ @@ -600,7 +605,7 @@ public class Alignment implements AlignmentI /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ @Override @@ -611,7 +616,7 @@ public class Alignment implements AlignmentI /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ @Override @@ -632,7 +637,7 @@ public class Alignment implements AlignmentI /** * DOCUMENT ME! - * + * * @param gc * DOCUMENT ME! */ @@ -652,7 +657,7 @@ public class Alignment implements AlignmentI /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ @Override @@ -663,7 +668,7 @@ public class Alignment implements AlignmentI /* * (non-Javadoc) - * + * * @see jalview.datamodel.AlignmentI#isAligned() */ @Override @@ -674,7 +679,7 @@ public class Alignment implements AlignmentI /* * (non-Javadoc) - * + * * @see jalview.datamodel.AlignmentI#isAligned(boolean) */ @Override @@ -701,7 +706,7 @@ public class Alignment implements AlignmentI /* * (non-Javadoc) - * + * * @seejalview.datamodel.AlignmentI#deleteAnnotation(jalview.datamodel. * AlignmentAnnotation) */ @@ -755,7 +760,7 @@ public class Alignment implements AlignmentI /** * remove any object references associated with this annotation - * + * * @param aa */ private void unhookAnnotation(AlignmentAnnotation aa) @@ -773,7 +778,7 @@ public class Alignment implements AlignmentI /* * (non-Javadoc) - * + * * @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel. * AlignmentAnnotation) */ @@ -785,7 +790,7 @@ public class Alignment implements AlignmentI /* * (non-Javadoc) - * + * * @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel. * AlignmentAnnotation, int) */ @@ -1005,7 +1010,7 @@ public class Alignment implements AlignmentI /** * Justify the sequences to the left or right by deleting and inserting gaps * before the initial residue or after the terminal residue - * + * * @param right * true if alignment padded to right, false to justify to left * @return true if alignment was changed @@ -1159,7 +1164,7 @@ public class Alignment implements AlignmentI /* * (non-Javadoc) - * + * * @see * jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame * ) @@ -1183,7 +1188,7 @@ public class Alignment implements AlignmentI /* * (non-Javadoc) - * + * * @see jalview.datamodel.AlignmentI#getCodonFrame(int) */ @Override @@ -1194,7 +1199,7 @@ public class Alignment implements AlignmentI /* * (non-Javadoc) - * + * * @see * jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI) */ @@ -1218,7 +1223,7 @@ public class Alignment implements AlignmentI /* * (non-Javadoc) - * + * * @see jalview.datamodel.AlignmentI#getCodonFrames() */ @Override @@ -1229,7 +1234,7 @@ public class Alignment implements AlignmentI /* * (non-Javadoc) - * + * * @seejalview.datamodel.AlignmentI#removeCodonFrame(jalview.datamodel. * AlignedCodonFrame) */ @@ -1381,21 +1386,27 @@ public class Alignment implements AlignmentI @Override public AlignmentAnnotation findOrCreateAnnotation(String name, - boolean autoCalc, SequenceI seqRef, SequenceGroup groupRef) + String calcId, boolean autoCalc, SequenceI seqRef, + SequenceGroup groupRef) { - for (AlignmentAnnotation annot : getAlignmentAnnotation()) + assert (name != null); + if (annotations != null) { - if (annot.autoCalculated == autoCalc - && annot.getCalcId().equals(name) - && annot.sequenceRef == seqRef && annot.groupRef == groupRef) + for (AlignmentAnnotation annot : getAlignmentAnnotation()) { - return annot; + if (annot.autoCalculated == autoCalc && (name.equals(annot.label)) + && (calcId == null || annot.getCalcId().equals(calcId)) + && annot.sequenceRef == seqRef + && annot.groupRef == groupRef) + { + return annot; + } } } AlignmentAnnotation annot = new AlignmentAnnotation(name, name, new Annotation[1], 0f, 0f, AlignmentAnnotation.BAR_GRAPH); annot.hasText = false; - annot.setCalcId(new String(name)); + annot.setCalcId(new String(calcId)); annot.autoCalculated = autoCalc; if (seqRef != null) { @@ -1473,5 +1484,32 @@ public class Alignment implements AlignmentI } } + @Override + public void validateAnnotation(AlignmentAnnotation alignmentAnnotation) + { + alignmentAnnotation.validateRangeAndDisplay(); + if (isNucleotide() && alignmentAnnotation.isValidStruc()) + { + hasRNAStructure = true; + } + } + @Override +public int getEndRes() +{ + return getWidth()-1; +}@Override +public int getStartRes() +{ + return 0; +} +/* In the case of AlignmentI - returns the dataset for the alignment, if set + * (non-Javadoc) + * @see jalview.datamodel.AnnotatedCollectionI#getContext() + */ +@Override +public AnnotatedCollectionI getContext() +{ + return dataset; +} }