X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=5315d1a2802f91ea0d93ceae9a9e9140b12d031d;hb=60403f610c291791bf7c58f9c7232206469687cd;hp=722edf21259bf2076967cd4906072f78d57fd7e6;hpb=45d4eb5f2d3772ac51e2512d49fb0a3a958f2260;p=jalview.git diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java index 722edf2..5315d1a 100755 --- a/src/jalview/datamodel/Sequence.java +++ b/src/jalview/datamodel/Sequence.java @@ -1,26 +1,28 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 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 + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8) + * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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.*; +import jalview.analysis.AlignSeq; + +import java.util.Enumeration; +import java.util.Vector; -import jalview.analysis.*; +import fr.orsay.lri.varna.models.rna.RNA; /** * @@ -48,6 +50,8 @@ public class Sequence implements SequenceI String vamsasId; DBRefEntry[] dbrefs; + + RNA rna; /** * This annotation is displayed below the alignment but the positions are tied @@ -55,21 +59,26 @@ public class Sequence implements SequenceI */ Vector annotation; - /** array of seuqence features - may not be null for a valid sequence object */ + /** + * The index of the sequence in a MSA + */ + int index = -1; + + /** array of sequence features - may not be null for a valid sequence object */ public SequenceFeature[] sequenceFeatures; /** * Creates a new Sequence object. * * @param name - * display name string + * display name string * @param sequence - * string to form a possibly gapped sequence out of + * string to form a possibly gapped sequence out of * @param start - * first position of non-gap residue in the sequence + * first position of non-gap residue in the sequence * @param end - * last position of ungapped residues (nearly always only used - * for display purposes) + * last position of ungapped residues (nearly always only used for + * display purposes) */ public Sequence(String name, String sequence, int start, int end) { @@ -117,7 +126,8 @@ public class Sequence implements SequenceI void checkValidRange() { - if (end < 1) + // Note: JAL-774 : + // http://issues.jalview.org/browse/JAL-774?focusedCommentId=11239&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-11239 { int endRes = 0; for (int j = 0; j < sequence.length; j++) @@ -132,7 +142,10 @@ public class Sequence implements SequenceI endRes += start - 1; } - this.end = endRes; + if (end < endRes) + { + end = endRes; + } } } @@ -141,9 +154,9 @@ public class Sequence implements SequenceI * Creates a new Sequence object. * * @param name - * DOCUMENT ME! + * DOCUMENT ME! * @param sequence - * DOCUMENT ME! + * DOCUMENT ME! */ public Sequence(String name, String sequence) { @@ -156,7 +169,7 @@ public class Sequence implements SequenceI * reference. * * @param seq - * DOCUMENT ME! + * DOCUMENT ME! */ public Sequence(SequenceI seq) { @@ -169,9 +182,9 @@ public class Sequence implements SequenceI * annotation that is present in the given annotation array. * * @param seq - * the sequence to be copied + * the sequence to be copied * @param alAnnotation - * an array of annotation including some associated with seq + * an array of annotation including some associated with seq */ public Sequence(SequenceI seq, AlignmentAnnotation[] alAnnotation) { @@ -185,15 +198,16 @@ public class Sequence implements SequenceI addSequenceFeature(new SequenceFeature(sf[i])); } } - if (seq.getDBRef() != null) + setDatasetSequence(seq.getDatasetSequence()); + if (datasetSequence == null && seq.getDBRef() != null) { + // only copy DBRefs if we really are a dataset sequence DBRefEntry[] dbr = seq.getDBRef(); for (int i = 0; i < dbr.length; i++) { addDBRef(new DBRefEntry(dbr[i])); } } - setDatasetSequence(seq.getDatasetSequence()); if (seq.getAnnotation() != null) { AlignmentAnnotation[] sqann = seq.getAnnotation(); @@ -234,7 +248,7 @@ public class Sequence implements SequenceI * DOCUMENT ME! * * @param v - * DOCUMENT ME! + * DOCUMENT ME! */ public void setSequenceFeatures(SequenceFeature[] features) { @@ -330,7 +344,7 @@ public class Sequence implements SequenceI * DOCUMENT ME! * * @param id - * DOCUMENT ME! + * DOCUMENT ME! */ public void setPDBId(Vector id) { @@ -367,7 +381,7 @@ public class Sequence implements SequenceI * DOCUMENT ME! * * @param name - * DOCUMENT ME! + * DOCUMENT ME! */ public void setName(String name) { @@ -389,7 +403,7 @@ public class Sequence implements SequenceI * DOCUMENT ME! * * @param start - * DOCUMENT ME! + * DOCUMENT ME! */ public void setStart(int start) { @@ -410,7 +424,7 @@ public class Sequence implements SequenceI * DOCUMENT ME! * * @param end - * DOCUMENT ME! + * DOCUMENT ME! */ public void setEnd(int end) { @@ -441,7 +455,7 @@ public class Sequence implements SequenceI * DOCUMENT ME! * * @param seq - * DOCUMENT ME! + * DOCUMENT ME! */ public void setSequence(String seq) { @@ -496,9 +510,9 @@ public class Sequence implements SequenceI * seqeunce * * @param start - * int + * int * @param end - * int + * int * @return SequenceI */ public SequenceI getSubSequence(int start, int end) @@ -532,7 +546,7 @@ public class Sequence implements SequenceI * DOCUMENT ME! * * @param i - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */ @@ -552,7 +566,7 @@ public class Sequence implements SequenceI * DOCUMENT ME! * * @param desc - * DOCUMENT ME! + * DOCUMENT ME! */ public void setDescription(String desc) { @@ -569,20 +583,17 @@ public class Sequence implements SequenceI return this.description; } - /** - * Return the alignment position for a sequence position - * - * @param pos - * lying from start to end + /* + * (non-Javadoc) * - * @return aligned position of residue pos + * @see jalview.datamodel.SequenceI#findIndex(int) */ public int findIndex(int pos) { // returns the alignment position for a residue int j = start; int i = 0; - + // Rely on end being at least as long as the length of the sequence. while ((i < sequence.length) && (j <= end) && (j <= pos)) { if (!jalview.util.Comparison.isGap(sequence[i])) @@ -607,7 +618,7 @@ public class Sequence implements SequenceI * Returns the sequence position for an alignment position * * @param i - * column index in alignment (from 1) + * column index in alignment (from 1) * * @return residue number for residue (left of and) nearest ith column */ @@ -660,6 +671,30 @@ public class Sequence implements SequenceI /* * (non-Javadoc) * + * @see jalview.datamodel.SequenceI#findPositionMap() + */ + public int[] findPositionMap() + { + int map[] = new int[sequence.length]; + int j = 0; + int pos = start; + int seqlen = sequence.length; + while ((j < seqlen)) + { + map[j] = pos; + if (!jalview.util.Comparison.isGap(sequence[j])) + { + pos++; + } + + j++; + } + return map; + } + + /* + * (non-Javadoc) + * * @see jalview.datamodel.SequenceI#deleteChars(int, int) */ public void deleteChars(int i, int j) @@ -715,7 +750,7 @@ public class Sequence implements SequenceI { createNewDs = true; newend--; // decrease end position by one for the deleted residue - // and search further + // and search further } } } @@ -740,11 +775,11 @@ public class Sequence implements SequenceI * DOCUMENT ME! * * @param i - * DOCUMENT ME! + * DOCUMENT ME! * @param c - * DOCUMENT ME! + * DOCUMENT ME! * @param chop - * DOCUMENT ME! + * DOCUMENT ME! */ public void insertCharAt(int i, int length, char c) { @@ -797,6 +832,11 @@ public class Sequence implements SequenceI public DBRefEntry[] getDBRef() { + if (dbrefs == null && datasetSequence != null + && this != datasetSequence) + { + return datasetSequence.getDBRef(); + } return dbrefs; } @@ -864,8 +904,10 @@ public class Sequence implements SequenceI { this.annotation = new Vector(); } - - this.annotation.addElement(annotation); + if (!this.annotation.contains(annotation)) + { + this.annotation.addElement(annotation); + } annotation.setSequenceRef(this); } @@ -961,8 +1003,9 @@ public class Sequence implements SequenceI /* * (non-Javadoc) * - * @see jalview.datamodel.SequenceI#setAlignmentAnnotation(AlignmmentAnnotation[] - * annotations) + * @see + * jalview.datamodel.SequenceI#setAlignmentAnnotation(AlignmmentAnnotation[] + * annotations) */ public void setAlignmentAnnotation(AlignmentAnnotation[] annotations) { @@ -1073,8 +1116,9 @@ public class Sequence implements SequenceI /* * (non-Javadoc) * - * @see jalview.datamodel.SequenceI#transferAnnotation(jalview.datamodel.SequenceI, - * jalview.datamodel.Mapping) + * @see + * jalview.datamodel.SequenceI#transferAnnotation(jalview.datamodel.SequenceI, + * jalview.datamodel.Mapping) */ public void transferAnnotation(SequenceI entry, Mapping mp) { @@ -1139,4 +1183,30 @@ public class Sequence implements SequenceI } } + /** + * @return The index (zero-based) on this sequence in the MSA. It returns + * {@code -1} if this information is not available. + */ + public int getIndex() + { + return index; + } + + /** + * Defines the position of this sequence in the MSA. Use the value {@code -1} + * if this information is undefined. + * + * @param The + * position for this sequence. This value is zero-based (zero for + * this first sequence) + */ + public void setIndex(int value) + { + index = value; + } + + public void setRNA(RNA r){rna=r;} + + public RNA getRNA() { return rna; } + }