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from develep
[jalview.git]
/
src
/
jalview
/
io
/
FeaturesFile.java
diff --git
a/src/jalview/io/FeaturesFile.java
b/src/jalview/io/FeaturesFile.java
index
12ad0d4
..
aa21b0f
100755
(executable)
--- a/
src/jalview/io/FeaturesFile.java
+++ b/
src/jalview/io/FeaturesFile.java
@@
-105,11
+105,11
@@
public class FeaturesFile extends AlignFile implements FeaturesSourceI
/**
* Constructor which does not parse the file immediately
*
/**
* Constructor which does not parse the file immediately
*
- * @param file
+ * @param file File or String filename
* @param paste
* @throws IOException
*/
* @param paste
* @throws IOException
*/
- public FeaturesFile(String file, DataSourceType paste)
+ public FeaturesFile(Object file, DataSourceType paste)
throws IOException
{
super(false, file, paste);
throws IOException
{
super(false, file, paste);
@@
-132,7
+132,7
@@
public class FeaturesFile extends AlignFile implements FeaturesSourceI
* @param type
* @throws IOException
*/
* @param type
* @throws IOException
*/
- public FeaturesFile(boolean parseImmediately, String file,
+ public FeaturesFile(boolean parseImmediately, Object file,
DataSourceType type) throws IOException
{
super(parseImmediately, file, type);
DataSourceType type) throws IOException
{
super(parseImmediately, file, type);
@@
-829,14
+829,15
@@
public class FeaturesFile extends AlignFile implements FeaturesSourceI
AlignViewportI av = getViewport();
if (av != null)
{
AlignViewportI av = getViewport();
if (av != null)
{
- if (av.getAlignment() != null)
+ AlignmentI a = av.getAlignment();
+ if (a != null)
{
{
- dataset = av.getAlignment().getDataset();
+ dataset = a.getDataset();
}
if (dataset == null)
{
// working in the applet context ?
}
if (dataset == null)
{
// working in the applet context ?
- dataset = av.getAlignment();
+ dataset = a;
}
}
else
}
}
else
@@
-890,7
+891,8
@@
public class FeaturesFile extends AlignFile implements FeaturesSourceI
StringBuilder out = new StringBuilder(256);
StringBuilder out = new StringBuilder(256);
- out.append(String.format("%s %d\n", GFF_VERSION, gffVersion == 0 ? 2 : gffVersion));
+ out.append(String.format("%s %d" + newline, GFF_VERSION,
+ gffVersion == 0 ? 2 : gffVersion));
if (!includeNonPositionalFeatures
&& (visibleColours == null || visibleColours.isEmpty()))
if (!includeNonPositionalFeatures
&& (visibleColours == null || visibleColours.isEmpty()))