/*
- * 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 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
{
// logger.error("Could not parse sequence line: " + line);
throw new IOException(MessageManager.formatMessage(
- "exception.couldnt_parse_sequence_line", new String[]
- { line }));
+ "exception.couldnt_parse_sequence_line",
+ new String[] { line }));
}
String ns = seqs.get(x.stringMatched(1));
if (ns == null)
}
else
{
- throw new IOException(MessageManager.formatMessage(
- "exception.error_parsing_line", new String[]
- { line }));
+ // throw new IOException(MessageManager.formatMessage(
+ // "exception.error_parsing_line", new String[] { line }));
+ System.err.println(">> missing annotation: " + line);
}
}
else if (annType.equals("GC"))
else
{
throw new IOException(MessageManager.formatMessage(
- "exception.unknown_annotation_detected", new String[]
- { annType, annContent }));
+ "exception.unknown_annotation_detected", new String[] {
+ annType, annContent }));
}
}
}
{
for (DBRefEntry d : dbrs)
{
- jalview.util.MapList mp = new jalview.util.MapList(new int[]
- { seqO.getStart(), seqO.getEnd() }, new int[]
- { st, en }, 1, 1);
+ jalview.util.MapList mp = new jalview.util.MapList(new int[] {
+ seqO.getStart(), seqO.getEnd() }, new int[] { st, en }, 1, 1);
jalview.datamodel.Mapping mping = new Mapping(mp);
d.setMap(mping);
}
// be written out
if (ss)
{
- //if (" .-_".indexOf(pos) == -1)
+ // if (" .-_".indexOf(pos) == -1)
{
if (detectbrackets.search(pos))
{
ann.displayCharacter = " " + ann.displayCharacter;
}
}
-
+
}
els[i] = ann;
{
feature = ds.getSequenceFeatures()[0].type;
}
+ // ?bug - feature may still have previous loop value
String key = type2id(feature);
if (key == null)
* @param ann
* @param sequenceI
*/
- private char outputCharacter(String key, int k,
- boolean isrna, Annotation[] ann, SequenceI sequenceI)
+ private char outputCharacter(String key, int k, boolean isrna,
+ Annotation[] ann, SequenceI sequenceI)
{
char seq = ' ';
Annotation annot = ann[k];
String ch = (annot == null) ? ((sequenceI == null) ? "-" : Character
- .toString(sequenceI.getCharAt(k)))
- : annot.displayCharacter;
+ .toString(sequenceI.getCharAt(k))) : annot.displayCharacter;
if (key != null && key.equals("SS"))
{
if (annot == null)
{
// sensible gap character if one is available or make one up
- return sequenceI == null ? '-' : sequenceI
- .getCharAt(k);
+ return sequenceI == null ? '-' : sequenceI.getCharAt(k);
}
else
{