X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2Fgff%2FGff3Helper.java;h=82e53132bbb15b4185850ec29eea293f3949942e;hb=70af62ad365829d2fc430db10336cf13c4d4ce1a;hp=031900d3c199d75b4f70e29b43abb07049ff7965;hpb=d3d566fbf876a3511c06fecec695b2f59eb71169;p=jalview.git
diff --git a/src/jalview/io/gff/Gff3Helper.java b/src/jalview/io/gff/Gff3Helper.java
index 031900d..82e5313 100644
--- a/src/jalview/io/gff/Gff3Helper.java
+++ b/src/jalview/io/gff/Gff3Helper.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.io.gff;
import jalview.datamodel.AlignedCodonFrame;
@@ -77,8 +97,8 @@ public class Gff3Helper extends GffHelperBase
}
else if (so.isA(soTerm, SequenceOntologyI.NUCLEOTIDE_MATCH))
{
- sf = processNucleotideMatch(attributes, seq, gff, align,
- newseqs, relaxedIdMatching);
+ sf = processNucleotideMatch(attributes, seq, gff, align, newseqs,
+ relaxedIdMatching);
}
else
{
@@ -92,7 +112,7 @@ public class Gff3Helper extends GffHelperBase
*/
sf = buildSequenceFeature(gff, null);
}
-
+
return sf;
}
@@ -119,8 +139,7 @@ public class Gff3Helper extends GffHelperBase
protected SequenceFeature processNucleotideMatch(
Map> attributes, SequenceI seq,
String[] gffColumns, AlignmentI align, List newseqs,
- boolean relaxedIdMatching)
- throws IOException
+ boolean relaxedIdMatching) throws IOException
{
String strand = gffColumns[STRAND_COL];
@@ -166,8 +185,8 @@ public class Gff3Helper extends GffHelperBase
* (new or existing) virtual sequence in the newseqs list
*/
String targetId = findTargetId(tokens[0], attributes);
- SequenceI mappedSequence1 = findSequence(targetId, align,
- newseqs, relaxedIdMatching);
+ SequenceI mappedSequence1 = findSequence(targetId, align, newseqs,
+ relaxedIdMatching);
SequenceI mappedSequence = mappedSequence1;
if (mappedSequence == null)
{
@@ -195,8 +214,7 @@ public class Gff3Helper extends GffHelperBase
int fromStart = Integer.parseInt(gffColumns[START_COL]);
int fromEnd = Integer.parseInt(gffColumns[END_COL]);
MapList mapping = constructMappingFromAlign(fromStart, fromEnd,
- toStart, toEnd,
- MappingType.NucleotideToNucleotide);
+ toStart, toEnd, MappingType.NucleotideToNucleotide);
if (mapping != null)
{
@@ -280,8 +298,8 @@ public class Gff3Helper extends GffHelperBase
for (String target : targets)
{
- SequenceI mappedSequence1 = findSequence(findTargetId(target, set), align,
- newseqs, relaxedIdMatching);
+ SequenceI mappedSequence1 = findSequence(findTargetId(target, set),
+ align, newseqs, relaxedIdMatching);
SequenceI mappedSequence = mappedSequence1;
if (mappedSequence == null)
{
@@ -379,8 +397,8 @@ public class Gff3Helper extends GffHelperBase
/*
* Ensembl returns dna variants as 'alleles'
*/
- desc = StringUtils.listToDelimitedString(
- attributes.get("alleles"), ",");
+ desc = StringUtils.listToDelimitedString(attributes.get("alleles"),
+ ",");
}
/*