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JAL-3761 listToArray became rangeListToArray
[jalview.git]
/
src
/
jalview
/
io
/
EmblFlatFile.java
diff --git
a/src/jalview/io/EmblFlatFile.java
b/src/jalview/io/EmblFlatFile.java
index
ff18a34
..
92af0df
100644
(file)
--- a/
src/jalview/io/EmblFlatFile.java
+++ b/
src/jalview/io/EmblFlatFile.java
@@
-50,10
+50,11
@@
public class EmblFlatFile extends AlignFile // FileParse
private static final String DOUBLED_QUOTE = QUOTE + QUOTE;
/**
private static final String DOUBLED_QUOTE = QUOTE + QUOTE;
/**
- * when true, interpret the mol_type 'source' feature attribute
- * and generate an RNA sequence from the DNA record
+ * when true, interpret the mol_type 'source' feature attribute and generate
+ * an RNA sequence from the DNA record
*/
*/
- private boolean produceRna=true;
+ private boolean produceRna = true;
+
/**
* A data bean class to hold values parsed from one CDS Feature (FT)
*/
/**
* A data bean class to hold values parsed from one CDS Feature (FT)
*/
@@
-91,7
+92,8
@@
public class EmblFlatFile extends AlignFile // FileParse
private List<DBRefEntry> dbrefs; // from DR
private List<DBRefEntry> dbrefs; // from DR
- private boolean sequenceStringIsRNA=false;
+ private boolean sequenceStringIsRNA = false;
+
private String sequenceString; // from SQ lines
/*
private String sequenceString; // from SQ lines
/*
@@
-323,11
+325,12
@@
public class EmblFlatFile extends AlignFile // FileParse
String parseFT(String line) throws IOException
{
String[] tokens = line.split(WHITESPACE);
String parseFT(String line) throws IOException
{
String[] tokens = line.split(WHITESPACE);
- if (tokens.length < 3 || (!"CDS".equals(tokens[1]) && !"source".equals(tokens[1])))
+ if (tokens.length < 3
+ || (!"CDS".equals(tokens[1]) && !"source".equals(tokens[1])))
{
return nextLine();
}
{
return nextLine();
}
-
+
if (tokens[1].equals("source"))
{
return parseSourceQualifiers(tokens);
if (tokens[1].equals("source"))
{
return parseSourceQualifiers(tokens);
@@
-432,8
+435,9
@@
public class EmblFlatFile extends AlignFile // FileParse
}
/**
}
/**
- * process attributes for 'source' until the next FT feature entry
- * only interested in 'mol_type'
+ * process attributes for 'source' until the next FT feature entry only
+ * interested in 'mol_type'
+ *
* @param tokens
* @return
* @throws IOException
* @param tokens
* @return
* @throws IOException
@@
-461,7
+465,7
@@
public class EmblFlatFile extends AlignFile // FileParse
int p = line.indexOf("\\mol_type");
int qs = line.indexOf("\"", p);
int qe = line.indexOf("\"", qs + 1);
int p = line.indexOf("\\mol_type");
int qs = line.indexOf("\"", p);
int qe = line.indexOf("\"", qs + 1);
- String qualifier=line.substring(qs,qe).toLowerCase();
+ String qualifier = line.substring(qs, qe).toLowerCase();
if (qualifier.indexOf("rna") > -1)
{
sequenceStringIsRNA = true;
if (qualifier.indexOf("rna") > -1)
{
sequenceStringIsRNA = true;
@@
-470,7
+474,7
@@
public class EmblFlatFile extends AlignFile // FileParse
{
sequenceStringIsRNA = false;
}
{
sequenceStringIsRNA = false;
}
- line=parseFeatureQualifier(sb, "source");
+ line = parseFeatureQualifier(sb, "source");
}
return line;
}
}
return line;
}
@@
-485,7
+489,7
@@
public class EmblFlatFile extends AlignFile // FileParse
*/
static String removeQuotes(String value)
{
*/
static String removeQuotes(String value)
{
- if (value == null)
+ if (value == null)
{
return null;
}
{
return null;
}
@@
-582,12
+586,12
@@
public class EmblFlatFile extends AlignFile // FileParse
{
name = this.sourceDb + "|" + name;
}
{
name = this.sourceDb + "|" + name;
}
-
+
if (produceRna && sequenceStringIsRNA)
{
sequenceString = sequenceString.replace('T', 'U').replace('t', 'u');
}
if (produceRna && sequenceStringIsRNA)
{
sequenceString = sequenceString.replace('T', 'U').replace('t', 'u');
}
-
+
SequenceI seq = new Sequence(name, this.sequenceString);
seq.setDescription(this.description);
SequenceI seq = new Sequence(name, this.sequenceString);
seq.setDescription(this.description);
@@
-861,7
+865,7
@@
public class EmblFlatFile extends AlignFile // FileParse
try
{
List<int[]> ranges = DnaUtils.parseLocation(location);
try
{
List<int[]> ranges = DnaUtils.parseLocation(location);
- return MappingUtils.listToArray(ranges);
+ return MappingUtils.rangeListToArray(ranges);
} catch (ParseException e)
{
Cache.log.warn(
} catch (ParseException e)
{
Cache.log.warn(