X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=5315d1a2802f91ea0d93ceae9a9e9140b12d031d;hb=60403f610c291791bf7c58f9c7232206469687cd;hp=21b877d4083609affa599393782ab5f92ad741a6;hpb=8666783ae3a3072f6c095c0f4d5037d4452afeb2;p=jalview.git diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java index 21b877d..5315d1a 100755 --- a/src/jalview/datamodel/Sequence.java +++ b/src/jalview/datamodel/Sequence.java @@ -1,13 +1,13 @@ /* - * 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) + * 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 @@ -22,6 +22,8 @@ import jalview.analysis.AlignSeq; import java.util.Enumeration; import java.util.Vector; +import fr.orsay.lri.varna.models.rna.RNA; + /** * * Implements the SequenceI interface for a char[] based sequence object. @@ -48,19 +50,21 @@ public class Sequence implements SequenceI String vamsasId; DBRefEntry[] dbrefs; + + RNA rna; /** * This annotation is displayed below the alignment but the positions are tied * to the residues of this sequence */ Vector annotation; - + /** - * The index of the sequence in a MSA + * The index of the sequence in a MSA */ int index = -1; - /** array of seuqence features - may not be null for a valid sequence object */ + /** array of sequence features - may not be null for a valid sequence object */ public SequenceFeature[] sequenceFeatures; /** @@ -122,7 +126,8 @@ public class Sequence implements SequenceI void checkValidRange() { - // Note: JAL-774 : http://issues.jalview.org/browse/JAL-774?focusedCommentId=11239&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-11239 + // 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++) @@ -137,7 +142,8 @@ public class Sequence implements SequenceI endRes += start - 1; } - if (end