/* * 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 */ package jalview.analysis; import java.util.*; import jalview.datamodel.*; /** *
Title:
* *Description:
* *Copyright: Copyright (c) 2004
* *Company: Dundee University
* * @author not attributable * @version 1.0 */ public class SeqsetUtils { /** * Store essential properties of a sequence in a hashtable for later recovery * Keys are Name, Start, End, SeqFeatures, PdbId * @param seq SequenceI * @return Hashtable */ public static Hashtable SeqCharacterHash(SequenceI seq) { Hashtable sqinfo = new Hashtable(); sqinfo.put("Name", seq.getName()); sqinfo.put("Start", new Integer(seq.getStart())); sqinfo.put("End", new Integer(seq.getEnd())); if (seq.getDescription() != null) { sqinfo.put("Description", seq.getDescription()); } Vector sfeat = new Vector(); jalview.datamodel.SequenceFeature[] sfarray = seq.getSequenceFeatures(); if (sfarray != null && sfarray.length > 0) { for (int i = 0; i < sfarray.length; i++) { sfeat.addElement(sfarray[i]); } } sqinfo.put("SeqFeatures", sfeat); sqinfo.put("PdbId", (seq.getPDBId() != null) ? seq.getPDBId() : new Vector()); sqinfo.put("datasetSequence", (seq.getDatasetSequence() != null) ? seq.getDatasetSequence() : new Sequence("THISISAPLACEHOLDER", "")); return sqinfo; } /** * Recover essential properties of a sequence from a hashtable * TODO: replace these methods with something more elegant. * @param sq SequenceI * @param sqinfo Hashtable * @return boolean true if name was not updated from sqinfo Name entry */ public static boolean SeqCharacterUnhash(SequenceI sq, Hashtable sqinfo) { boolean namePresent = true; if (sqinfo == null) { return false; } String oldname = (String) sqinfo.get("Name"); Integer start = (Integer) sqinfo.get("Start"); Integer end = (Integer) sqinfo.get("End"); Vector sfeatures = (Vector) sqinfo.get( "SeqFeatures"); Vector pdbid = (Vector) sqinfo.get("PdbId"); String description = (String) sqinfo.get("Description"); Sequence seqds = (Sequence) sqinfo.get("datasetSequence"); if (oldname == null) { namePresent = false; } else { sq.setName(oldname); } if (pdbid != null && pdbid.size() > 0) { sq.setPDBId(pdbid); } if ( (start != null) && (end != null)) { sq.setStart(start.intValue()); sq.setEnd(end.intValue()); } if ( (sfeatures != null) && (sfeatures.size() > 0)) { SequenceFeature[] sfarray = new SequenceFeature[sfeatures.size()]; for (int is=0,isize=sfeatures.size();is