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JAL-2189 source formatting
[jalview.git]
/
src
/
jalview
/
io
/
gff
/
ExonerateHelper.java
diff --git
a/src/jalview/io/gff/ExonerateHelper.java
b/src/jalview/io/gff/ExonerateHelper.java
index
e373861
..
1ee99c0
100644
(file)
--- a/
src/jalview/io/gff/ExonerateHelper.java
+++ b/
src/jalview/io/gff/ExonerateHelper.java
@@
-41,7
+41,7
@@
public class ExonerateHelper extends Gff2Helper
*
* @param seq
* the sequence with which this feature is associated
*
* @param seq
* the sequence with which this feature is associated
- * @param sf
+ * @param gffColumns
* the sequence feature with ATTRIBUTES property containing any
* additional attributes
* @param align
* the sequence feature with ATTRIBUTES property containing any
* additional attributes
* @param align
@@
-64,8
+64,8
@@
public class ExonerateHelper extends Gff2Helper
try
{
try
{
- processGffSimilarity(set, seq, gffColumns,
- align, newseqs, relaxedIdMatching);
+ processGffSimilarity(set, seq, gffColumns, align, newseqs,
+ relaxedIdMatching);
} catch (IOException ivfe)
{
System.err.println(ivfe);
} catch (IOException ivfe)
{
System.err.println(ivfe);
@@
-98,8
+98,7
@@
public class ExonerateHelper extends Gff2Helper
* if true allow fuzzy search for a matching target sequence
* @throws IOException
*/
* if true allow fuzzy search for a matching target sequence
* @throws IOException
*/
- protected void processGffSimilarity(
- Map<String, List<String>> set,
+ protected void processGffSimilarity(Map<String, List<String>> set,
SequenceI seq, String[] gff, AlignmentI align,
List<SequenceI> newseqs, boolean relaxedIdMatching)
throws IOException
SequenceI seq, String[] gff, AlignmentI align,
List<SequenceI> newseqs, boolean relaxedIdMatching)
throws IOException
@@
-167,7
+166,7
@@
public class ExonerateHelper extends Gff2Helper
mapToSequence);
/*
mapToSequence);
/*
- * exonerate GFF has the strand of the target in column 7 rather
+ * exonerate GFF has the strand of the target in column 7
* (differs from GFF3 which has it in the Target descriptor)
*/
String strand = gff[STRAND_COL];
* (differs from GFF3 which has it in the Target descriptor)
*/
String strand = gff[STRAND_COL];
@@
-228,15
+227,17
@@
public class ExonerateHelper extends Gff2Helper
int alignFromStart;
int alignToStart;
int alignCount;
int alignFromStart;
int alignToStart;
int alignCount;
- try {
+ try
+ {
alignFromStart = Integer.parseInt(tokens[0]);
alignToStart = Integer.parseInt(tokens[1]);
alignCount = Integer.parseInt(tokens[2]);
alignFromStart = Integer.parseInt(tokens[0]);
alignToStart = Integer.parseInt(tokens[1]);
alignCount = Integer.parseInt(tokens[2]);
- } catch (NumberFormatException nfe) {
+ } catch (NumberFormatException nfe)
+ {
System.err.println(nfe.toString());
return null;
}
System.err.println(nfe.toString());
return null;
}
-
+
int fromStart;
int fromEnd;
int toStart;
int fromStart;
int fromEnd;
int toStart;
@@
-290,10
+291,8
@@
public class ExonerateHelper extends Gff2Helper
{
result = MappingType.PeptideToNucleotide;
}
{
result = MappingType.PeptideToNucleotide;
}
- else if (model.contains(CODING2CODING)
- || model.contains(CODING2GENOME)
- || model.contains(CDNA2GENOME)
- || model.contains(GENOME2GENOME))
+ else if (model.contains(CODING2CODING) || model.contains(CODING2GENOME)
+ || model.contains(CDNA2GENOME) || model.contains(GENOME2GENOME))
{
result = MappingType.NucleotideToNucleotide;
}
{
result = MappingType.NucleotideToNucleotide;
}
@@
-304,7
+303,7
@@
public class ExonerateHelper extends Gff2Helper
* Tests whether the GFF data looks like it was generated by exonerate, and is
* a format we are willing to handle
*
* Tests whether the GFF data looks like it was generated by exonerate, and is
* a format we are willing to handle
*
- * @param sf
+ * @param columns
* @return
*/
public static boolean recognises(String[] columns)
* @return
*/
public static boolean recognises(String[] columns)
@@
-323,10
+322,8
@@
public class ExonerateHelper extends Gff2Helper
{
String mdl = model.toLowerCase();
if (mdl.contains(PROTEIN2DNA) || mdl.contains(PROTEIN2GENOME)
{
String mdl = model.toLowerCase();
if (mdl.contains(PROTEIN2DNA) || mdl.contains(PROTEIN2GENOME)
- || mdl.contains(CODING2CODING)
- || mdl.contains(CODING2GENOME)
- || mdl.contains(CDNA2GENOME)
- || mdl.contains(GENOME2GENOME))
+ || mdl.contains(CODING2CODING) || mdl.contains(CODING2GENOME)
+ || mdl.contains(CDNA2GENOME) || mdl.contains(GENOME2GENOME))
{
return true;
}
{
return true;
}