X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fio%2Fgff%2FGffHelperBase.java;h=1d4d3acbe8c90e25f3003dae372a2452789873e2;hb=8de672a19aa66c59e84511da1961dd35397c02cb;hp=feeec1d2a60c7a87c5e678f87b8acbecb7956793;hpb=b4fac54ddfb91688f281a6a2ede0d8d44ec1dd13;p=jalview.git
diff --git a/src/jalview/io/gff/GffHelperBase.java b/src/jalview/io/gff/GffHelperBase.java
index feeec1d..1d4d3ac 100644
--- a/src/jalview/io/gff/GffHelperBase.java
+++ b/src/jalview/io/gff/GffHelperBase.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.analysis.SequenceIdMatcher;
@@ -130,8 +150,8 @@ public abstract class GffHelperBase implements GffHelperI
* restrict from range to make them match up
* it's kind of arbitrary which end we truncate - here it is the end
*/
- System.err.print("Truncating mapping from " + Arrays.toString(from)
- + " to ");
+ System.err.print(
+ "Truncating mapping from " + Arrays.toString(from) + " to ");
if (from[1] > from[0])
{
from[1] -= fromOverlap / toRatio;
@@ -149,8 +169,8 @@ public abstract class GffHelperBase implements GffHelperI
/*
* restrict to range to make them match up
*/
- System.err.print("Truncating mapping to " + Arrays.toString(to)
- + " to ");
+ System.err.print(
+ "Truncating mapping to " + Arrays.toString(to) + " to ");
if (to[1] > to[0])
{
to[1] -= fromOverlap / fromRatio;
@@ -241,7 +261,8 @@ public abstract class GffHelperBase implements GffHelperI
/**
* Parses the input line to a map of name / value(s) pairs. For example the
* line
- * Notes=Fe-S;Method=manual curation, prediction; source = Pfam; Notes = Metal
+ * Notes=Fe-S;Method=manual curation, prediction; source = Pfam; Notes = Metal
+ *
* if parsed with delimiter=";" and separators {' ', '='}
* would return a map with { Notes={Fe=S, Metal}, Method={manual curation,
* prediction}, source={Pfam}}
@@ -317,6 +338,19 @@ public abstract class GffHelperBase implements GffHelperI
protected SequenceFeature buildSequenceFeature(String[] gff,
Map> attributes)
{
+ return buildSequenceFeature(gff, TYPE_COL, gff[SOURCE_COL], attributes);
+ }
+
+ /**
+ * @param gff
+ * @param typeColumn
+ * @param group
+ * @param attributes
+ * @return
+ */
+ protected SequenceFeature buildSequenceFeature(String[] gff,
+ int typeColumn, String group, Map> attributes)
+ {
try
{
int start = Integer.parseInt(gff[START_COL]);
@@ -335,8 +369,8 @@ public abstract class GffHelperBase implements GffHelperI
// e.g. '.' - leave as zero
}
- SequenceFeature sf = new SequenceFeature(gff[TYPE_COL],
- gff[SOURCE_COL], start, end, score, gff[SOURCE_COL]);
+ SequenceFeature sf = new SequenceFeature(gff[typeColumn],
+ gff[SOURCE_COL], start, end, score, group);
sf.setStrand(gff[STRAND_COL]);
@@ -355,8 +389,8 @@ public abstract class GffHelperBase implements GffHelperI
*/
for (Entry> attr : attributes.entrySet())
{
- String values = StringUtils.listToDelimitedString(
- attr.getValue(), ",");
+ String values = StringUtils.listToDelimitedString(attr.getValue(),
+ ",");
sf.setValue(attr.getKey(), values);
if (NOTE.equals(attr.getKey()))
{
@@ -392,7 +426,8 @@ public abstract class GffHelperBase implements GffHelperI
* @param toSeq
* @return
*/
- protected AlignedCodonFrame getMapping(AlignmentI align, SequenceI fromSeq, SequenceI toSeq)
+ protected AlignedCodonFrame getMapping(AlignmentI align,
+ SequenceI fromSeq, SequenceI toSeq)
{
AlignedCodonFrame acf = align.getMapping(fromSeq, toSeq);
if (acf == null)