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145c060
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added (and enabled) switch to store gff source string as sequencefeature.group rather...
author
jprocter
<Jim Procter>
Mon, 15 Dec 2008 10:35:09 +0000
(10:35 +0000)
committer
jprocter
<Jim Procter>
Mon, 15 Dec 2008 10:35:09 +0000
(10:35 +0000)
src/jalview/io/FeaturesFile.java
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diff --git
a/src/jalview/io/FeaturesFile.java
b/src/jalview/io/FeaturesFile.java
index
5058e5f
..
17ff88f
100755
(executable)
--- a/
src/jalview/io/FeaturesFile.java
+++ b/
src/jalview/io/FeaturesFile.java
@@
-36,6
+36,11
@@
import jalview.schemes.*;
public class FeaturesFile extends AlignFile
\r
{
\r
/**
\r
public class FeaturesFile extends AlignFile
\r
{
\r
/**
\r
+ * work around for GFF interpretation bug where source string becomes description rather than a group
\r
+ */
\r
+ private boolean doGffSource = true;
\r
+
\r
+ /**
\r
* Creates a new FeaturesFile object.
\r
*/
\r
public FeaturesFile()
\r
* Creates a new FeaturesFile object.
\r
*/
\r
public FeaturesFile()
\r
@@
-161,17
+166,34
@@
public class FeaturesFile extends AlignFile
if (seq != null)
\r
{
\r
desc = st.nextToken();
\r
if (seq != null)
\r
{
\r
desc = st.nextToken();
\r
+ String group=null;
\r
+ if (doGffSource && desc.indexOf(' ')==-1) {
\r
+ // could also be a source term rather than description line
\r
+ group = new String(desc);
\r
+ }
\r
type = st.nextToken();
\r
try
\r
{
\r
type = st.nextToken();
\r
try
\r
{
\r
- start = Integer.parseInt(st.nextToken());
\r
+ String stt = st.nextToken();
\r
+ if (stt.length()==0 || stt.equals("-"))
\r
+ {
\r
+ start = 0;
\r
+ } else {
\r
+ start = Integer.parseInt(stt);
\r
+ }
\r
} catch (NumberFormatException ex)
\r
{
\r
start = 0;
\r
}
\r
try
\r
{
\r
} catch (NumberFormatException ex)
\r
{
\r
start = 0;
\r
}
\r
try
\r
{
\r
- end = Integer.parseInt(st.nextToken());
\r
+ String stt = st.nextToken();
\r
+ if (stt.length()==0 || stt.equals("-"))
\r
+ {
\r
+ end = -1;
\r
+ } else {
\r
+ end = Integer.parseInt(stt);
\r
+ }
\r
} catch (NumberFormatException ex)
\r
{
\r
end = -1;
\r
} catch (NumberFormatException ex)
\r
{
\r
end = -1;
\r
@@
-184,7
+206,7
@@
public class FeaturesFile extends AlignFile
score = 0;
\r
}
\r
\r
score = 0;
\r
}
\r
\r
- sf = new SequenceFeature(type, desc, start, end, score, null);
\r
+ sf = new SequenceFeature(type, desc, start, end, score, group);
\r
\r
try
\r
{
\r
\r
try
\r
{
\r