From d6c464dcc3c70d07a756ceef49971e212e8b5876 Mon Sep 17 00:00:00 2001 From: jprocter Date: Fri, 16 Sep 2011 11:30:36 +0100 Subject: [PATCH 1/1] patch for JAL-935 - warning messages raised when alignment and tree leaves are not proper subsets of either. --- src/jalview/analysis/AlignmentSorter.java | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java index 158fe81..797af0c 100755 --- a/src/jalview/analysis/AlignmentSorter.java +++ b/src/jalview/analysis/AlignmentSorter.java @@ -456,15 +456,15 @@ public class AlignmentSorter // TODO: JBPNote - decide if this is always an error // (eg. not when a tree is associated to another alignment which has more // sequences) - if (tmp.size() < nSeq) + if (tmp.size() != nSeq) { addStrays(align, tmp); } if (tmp.size() != nSeq) { - System.err.println("ERROR: tmp.size()=" + tmp.size() + " != nseq=" - + nSeq + " in getOrderByTree"); + System.err.println("WARNING: tmp.size()=" + tmp.size() + " != nseq=" + + nSeq + " in getOrderByTree - tree contains sequences not in alignment"); } } @@ -560,7 +560,7 @@ public class AlignmentSorter { if (node.element() instanceof SequenceI) { - if (!tmp.contains(node.element())) + if (!tmp.contains(node.element())) // && (seqset==null || seqset.size()==0 || seqset.contains(tmp))) { tmp.addElement((SequenceI) node.element()); } -- 1.7.10.2