X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FSeqsetUtils.java;h=a86775d5c4e44f46eb7fd23ad002ff395cc71fbb;hb=506d60f0e188723ddc91c26824b41ac7034df3fe;hp=0aa2bd5e359f63e1a4ae4dcf6982ca219bf478df;hpb=60f2d6c034560415fd0139c8bc7df0c19cae1186;p=jalview.git diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java index 0aa2bd5..a86775d 100755 --- a/src/jalview/analysis/SeqsetUtils.java +++ b/src/jalview/analysis/SeqsetUtils.java @@ -1,17 +1,17 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) + * Copyright (C) 2008 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 @@ -23,14 +23,22 @@ import java.util.*; import jalview.datamodel.*; /** - *
Title:
- * - *Description:
- * - *Copyright: Copyright (c) 2004
- * - *Company: Dundee University
- * + *+ * Title: + *
+ * + *+ * Description: + *
+ * + *+ * Copyright: Copyright (c) 2004 + *
+ * + *+ * Company: Dundee University + *
+ * * @author not attributable * @version 1.0 */ @@ -39,8 +47,10 @@ 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 + * Keys are Name, Start, End, SeqFeatures, PdbId + * + * @param seq + * SequenceI * @return Hashtable */ public static Hashtable SeqCharacterHash(SequenceI seq) @@ -63,19 +73,21 @@ public class SeqsetUtils } } 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", "")); + 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 + * 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) @@ -88,8 +100,7 @@ public class SeqsetUtils 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 sfeatures = (Vector) sqinfo.get("SeqFeatures"); Vector pdbid = (Vector) sqinfo.get("PdbId"); String description = (String) sqinfo.get("Description"); Sequence seqds = (Sequence) sqinfo.get("datasetSequence"); @@ -106,17 +117,17 @@ public class SeqsetUtils sq.setPDBId(pdbid); } - if ( (start != null) && (end != null)) + if ((start != null) && (end != null)) { sq.setStart(start.intValue()); sq.setEnd(end.intValue()); } - if ( (sfeatures != null) && (sfeatures.size() > 0)) + if ((sfeatures != null) && (sfeatures.size() > 0)) { SequenceFeature[] sfarray = new SequenceFeature[sfeatures.size()]; - for (int is=0,isize=sfeatures.size();is