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JAL-1260 refactored multi-line qualifier separators
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Tue, 18 Aug 2020 14:32:00 +0000
(15:32 +0100)
committer
gmungoc
<g.m.carstairs@dundee.ac.uk>
Tue, 18 Aug 2020 14:32:00 +0000
(15:32 +0100)
src/jalview/io/FlatFile.java
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diff --git
a/src/jalview/io/FlatFile.java
b/src/jalview/io/FlatFile.java
index
c247601
..
4c1777c
100644
(file)
--- a/
src/jalview/io/FlatFile.java
+++ b/
src/jalview/io/FlatFile.java
@@
-215,7
+215,7
@@
public abstract class FlatFile extends AlignFile
*/
CdsData data = new CdsData();
StringBuilder sb = new StringBuilder().append(location);
*/
CdsData data = new CdsData();
StringBuilder sb = new StringBuilder().append(location);
- line = parseFeatureQualifier(sb, LOCATION);
+ line = parseFeatureQualifier(sb, false);
data.cdsLocation = sb.toString();
while (line != null)
data.cdsLocation = sb.toString();
while (line != null)
@@
-250,7
+250,8
@@
public abstract class FlatFile extends AlignFile
String value = line.substring(eqPos + 1);
value = removeQuotes(value);
sb = new StringBuilder().append(value);
String value = line.substring(eqPos + 1);
value = removeQuotes(value);
sb = new StringBuilder().append(value);
- line = parseFeatureQualifier(sb, qualifier);
+ boolean asText = !"translation".equals(qualifier);
+ line = parseFeatureQualifier(sb, asText);
String featureValue = sb.toString();
if ("protein_id".equals(qualifier))
String featureValue = sb.toString();
if ("protein_id".equals(qualifier))
@@
-638,11
+639,11
@@
public abstract class FlatFile extends AlignFile
*
* @param sb
* a string buffer primed with the first line of the value
*
* @param sb
* a string buffer primed with the first line of the value
- * @param qualifierName
+ * @param asText
* @return
* @throws IOException
*/
* @return
* @throws IOException
*/
- String parseFeatureQualifier(StringBuilder sb, String qualifierName)
+ String parseFeatureQualifier(StringBuilder sb, boolean asText)
throws IOException
{
String line;
throws IOException
{
String line;
@@
-665,11
+666,10
@@
public abstract class FlatFile extends AlignFile
}
/*
}
/*
- * heuristic rule: most multi-line value (e.g. /product) are text,
- * so add a space for word boundary at a new line; not for translation
+ * if text (e.g. /product), add a word separator for a new line,
+ * else (e.g. /translation) don't
*/
*/
- if (!"translation".equals(qualifierName)
- && !LOCATION.equals(qualifierName))
+ if (asText)
{
sb.append(" ");
}
{
sb.append(" ");
}