X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FSeqsetUtils.java;h=21dea5793b0b56306c1fcf51c0ba995d6b2b3669;hb=e9aa1cee679000405c5549829ee08e1c08b2ffd5;hp=0aa2bd5e359f63e1a4ae4dcf6982ca219bf478df;hpb=ccc0d91abe38690088a6050faba8ef66cde1f271;p=jalview.git
diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index 0aa2bd5..21dea57 100755
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -1,20 +1,19 @@
/*
- * 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 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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
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 + * Keys are Name, Start, End, SeqFeatures, PdbId + * + * @param seq + * SequenceI * @return Hashtable */ public static Hashtable SeqCharacterHash(SequenceI seq) @@ -63,19 +52,22 @@ public class SeqsetUtils } } sqinfo.put("SeqFeatures", sfeat); - sqinfo.put("PdbId", - (seq.getPDBId() != null) ? seq.getPDBId() : new Vector()); + sqinfo.put("PdbId", (seq.getPDBId() != null) ? seq.getPDBId() + : new Vector()); sqinfo.put("datasetSequence", - (seq.getDatasetSequence() != null) ? seq.getDatasetSequence() : - new Sequence("THISISAPLACEHOLDER", "")); + (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 +80,7 @@ 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 +97,17 @@ 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