X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FBLCFile.java;h=a499f750f8187e1d91f95db282ed74ceb2788419;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=66f9d8e322904308f1e9ef5e4df22ddd7ff3a941;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git diff --git a/src/jalview/io/BLCFile.java b/src/jalview/io/BLCFile.java index 66f9d8e..a499f75 100755 --- a/src/jalview/io/BLCFile.java +++ b/src/jalview/io/BLCFile.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,10 +20,11 @@ */ package jalview.io; -import java.io.*; -import java.util.*; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceI; -import jalview.datamodel.*; +import java.io.IOException; +import java.util.Vector; /** * DOCUMENT ME! @@ -115,7 +116,9 @@ public class BLCFile extends AlignFile { line = nextLine(); if (line == null) + { break; + } // seek end of ids if (line.indexOf("*") > -1) { @@ -150,7 +153,9 @@ public class BLCFile extends AlignFile } } while (!idsFound); if (line == null) + { break; // end of file. + } int starCol = line.indexOf("*"); seqstrings = new StringBuffer[seqs.size()]; @@ -198,9 +203,11 @@ public class BLCFile extends AlignFile } if (seqs.size() > 0) { - if (headerLines.length() > 1 + numHeaderLines) // could see if buffer is + if (headerLines.length() > 1 + numHeaderLines) + { // just whitespace or not. setAlignmentProperty("Comments", headerLines.toString()); + } setAlignmentProperty("iteration", "" + iterationCount); } }