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JAL-3438 spotless for 2.11.2.0
[jalview.git]
/
src
/
jalview
/
io
/
EMBLLikeFlatFile.java
diff --git
a/src/jalview/io/EMBLLikeFlatFile.java
b/src/jalview/io/EMBLLikeFlatFile.java
index
e8ce34b
..
7671412
100644
(file)
--- a/
src/jalview/io/EMBLLikeFlatFile.java
+++ b/
src/jalview/io/EMBLLikeFlatFile.java
@@
-160,8
+160,7
@@
public abstract class EMBLLikeFlatFile extends AlignFile
* 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
*/
- protected boolean produceRna=true;
-
+ protected boolean produceRna = true;
/*
* values parsed from the data file
/*
* values parsed from the data file
@@
-178,7
+177,7
@@
public abstract class EMBLLikeFlatFile extends AlignFile
protected List<DBRefEntry> dbrefs;
protected List<DBRefEntry> dbrefs;
- protected boolean sequenceStringIsRNA=false;
+ protected boolean sequenceStringIsRNA = false;
protected String sequenceString;
protected String sequenceString;
@@
-201,13
+200,14
@@
public abstract class EMBLLikeFlatFile extends AlignFile
* using TreeMap gives CDS sequences in alphabetical, so readable, order
*/
cds = new TreeMap<>(String.CASE_INSENSITIVE_ORDER);
* using TreeMap gives CDS sequences in alphabetical, so readable, order
*/
cds = new TreeMap<>(String.CASE_INSENSITIVE_ORDER);
-
+
parse();
}
/**
parse();
}
/**
- * 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
@@
-236,7
+236,7
@@
public abstract class EMBLLikeFlatFile extends AlignFile
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(Locale.ROOT);
+ String qualifier = line.substring(qs, qe).toLowerCase(Locale.ROOT);
if (qualifier.indexOf("rna") > -1)
{
sequenceStringIsRNA = true;
if (qualifier.indexOf("rna") > -1)
{
sequenceStringIsRNA = true;
@@
-245,12
+245,11
@@
public abstract class EMBLLikeFlatFile extends AlignFile
{
sequenceStringIsRNA = false;
}
{
sequenceStringIsRNA = false;
}
- line=parseFeatureQualifier(sb, false);
+ line = parseFeatureQualifier(sb, false);
}
return line;
}
}
return line;
}
-
/**
* Parses one (GenBank or EMBL format) CDS feature, saves the parsed data, and
* returns the next line
/**
* Parses one (GenBank or EMBL format) CDS feature, saves the parsed data, and
* returns the next line
@@
-715,8
+714,8
@@
public abstract class EMBLLikeFlatFile extends AlignFile
String[] tokens = line.split(WHITESPACE);
if (tokens.length < 2)
{
String[] tokens = line.split(WHITESPACE);
if (tokens.length < 2)
{
- Console.error("Ignoring bad EMBL line for " + this.accession
- + ": " + line);
+ Console.error("Ignoring bad EMBL line for " + this.accession + ": "
+ + line);
break;
}
if (tokens[1].startsWith("/"))
break;
}
if (tokens[1].startsWith("/"))
@@
-797,7
+796,8
@@
public abstract class EMBLLikeFlatFile extends AlignFile
protected String parseFeature(String line) throws IOException
{
String[] tokens = line.trim().split(WHITESPACE);
protected String parseFeature(String line) throws IOException
{
String[] tokens = line.trim().split(WHITESPACE);
- if (tokens.length < 2 || (!"CDS".equals(tokens[0]) && (!"source".equals(tokens[0]))))
+ if (tokens.length < 2
+ || (!"CDS".equals(tokens[0]) && (!"source".equals(tokens[0]))))
{
return nextLine();
}
{
return nextLine();
}