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JAL-1641 cherry-picked changes into develop compatible branch
[jalview.git]
/
src
/
jalview
/
io
/
FormatAdapter.java
diff --git
a/src/jalview/io/FormatAdapter.java
b/src/jalview/io/FormatAdapter.java
index
df5353c
..
74410a1
100755
(executable)
--- a/
src/jalview/io/FormatAdapter.java
+++ b/
src/jalview/io/FormatAdapter.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-259,17
+259,20
@@
public class FormatAdapter extends AppletFormatAdapter
throws java.io.IOException
{
Alignment al;
throws java.io.IOException
{
Alignment al;
- if (format.equals("HTML"))
+ if (format.equals(JSONFile.FILE_DESC))
{
{
- afile = new HtmlFile(inFile, type);
+ afile = new JSONFile(inFile, type);
al = new Alignment(afile.getSeqsAsArray());
afile.addAnnotations(al);
al = new Alignment(afile.getSeqsAsArray());
afile.addAnnotations(al);
+ for (SequenceGroup sg : afile.getSeqGroups())
+ {
+ al.addGroup(sg);
+ }
}
else
{
al = super.readFile(inFile, type, format);
}
}
else
{
al = super.readFile(inFile, type, format);
}
-
return al;
}
return al;
}
@@
-277,11
+280,12
@@
public class FormatAdapter extends AppletFormatAdapter
throws java.io.IOException
{
Alignment al;
throws java.io.IOException
{
Alignment al;
- if (format.equals("HTML"))
+ if (format.equals(JSONFile.FILE_DESC))
{
{
- afile = new HtmlFile(source);
+ afile = new JSONFile(source);
al = new Alignment(afile.getSeqsAsArray());
afile.addAnnotations(al);
al = new Alignment(afile.getSeqsAsArray());
afile.addAnnotations(al);
+ afile.addSeqGroups(al);
}
else
{
}
else
{
@@
-323,4
+327,5
@@
public class FormatAdapter extends AppletFormatAdapter
return formatSequences(format, getCacheSuffixDefault(format), av, selectedOnly);
}
return formatSequences(format, getCacheSuffixDefault(format), av, selectedOnly);
}
+
}
}