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Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of https://source.jalview.org/git...
[jalview.git]
/
src
/
jalview
/
io
/
AnnotationFile.java
diff --git
a/src/jalview/io/AnnotationFile.java
b/src/jalview/io/AnnotationFile.java
index
e578a45
..
6b02022
100755
(executable)
--- a/
src/jalview/io/AnnotationFile.java
+++ b/
src/jalview/io/AnnotationFile.java
@@
-646,7
+646,7
@@
public class AnnotationFile
String refSeqId = null;
String refSeqId = null;
- public boolean annotateAlignmentView(AlignViewportI viewport, String file,
+ public boolean annotateAlignmentView(AlignViewportI viewport, Object file,
DataSourceType protocol)
{
ColumnSelection colSel = viewport.getColumnSelection();
DataSourceType protocol)
{
ColumnSelection colSel = viewport.getColumnSelection();
@@
-677,23
+677,23
@@
public class AnnotationFile
}
public boolean readAnnotationFile(AlignmentI al, HiddenColumns hidden,
}
public boolean readAnnotationFile(AlignmentI al, HiddenColumns hidden,
- String file, DataSourceType sourceType)
+ Object file, DataSourceType sourceType)
{
BufferedReader in = null;
try
{
if (sourceType == DataSourceType.FILE)
{
{
BufferedReader in = null;
try
{
if (sourceType == DataSourceType.FILE)
{
- in = new BufferedReader(new FileReader(file));
+ in = FileLoader.getBuffereReader(file);
}
else if (sourceType == DataSourceType.URL)
{
}
else if (sourceType == DataSourceType.URL)
{
- URL url = new URL(file);
+ URL url = new URL(file.toString());
in = new BufferedReader(new InputStreamReader(url.openStream()));
}
else if (sourceType == DataSourceType.PASTE)
{
in = new BufferedReader(new InputStreamReader(url.openStream()));
}
else if (sourceType == DataSourceType.PASTE)
{
- in = new BufferedReader(new StringReader(file));
+ in = new BufferedReader(new StringReader(file.toString()));
}
else if (sourceType == DataSourceType.CLASSLOADER)
{
}
else if (sourceType == DataSourceType.CLASSLOADER)
{