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JAL-653 JAL-1780 refactor getGroups so HTMLfile/JSONfile adopt same pattern as other...
[jalview.git]
/
src
/
jalview
/
io
/
AppletFormatAdapter.java
diff --git
a/src/jalview/io/AppletFormatAdapter.java
b/src/jalview/io/AppletFormatAdapter.java
index
1633212
..
7810771
100755
(executable)
--- a/
src/jalview/io/AppletFormatAdapter.java
+++ b/
src/jalview/io/AppletFormatAdapter.java
@@
-285,26
+285,10
@@
public class AppletFormatAdapter
else if (format.equals(JSONFile.FILE_DESC))
{
alignFile = new JSONFile(inFile, type);
else if (format.equals(JSONFile.FILE_DESC))
{
alignFile = new JSONFile(inFile, type);
- al = new Alignment(alignFile.getSeqsAsArray());
- alignFile.addAnnotations(al);
- ((JSONFile) alignFile).setViewport(viewport);
- for (SequenceGroup sg : alignFile.getSeqGroups())
- {
- al.addGroup(sg);
- }
-
- return al;
}
else if (format.equals(HtmlFile.FILE_DESC))
{
alignFile = new HtmlFile(inFile, type);
}
else if (format.equals(HtmlFile.FILE_DESC))
{
alignFile = new HtmlFile(inFile, type);
- al = new Alignment(alignFile.getSeqsAsArray());
- alignFile.addAnnotations(al);
- for (SequenceGroup sg : alignFile.getSeqGroups())
- {
- al.addGroup(sg);
- }
- return al;
}
else if (format.equals("RNAML"))
{
}
else if (format.equals("RNAML"))
{
@@
-314,11
+298,15
@@
public class AppletFormatAdapter
{
alignFile = new Gff3File(inFile, type);
}
{
alignFile = new Gff3File(inFile, type);
}
-
+ // Standard boilerplate for creating alignment from parser
+ alignFile.setViewport(viewport);
+
al = new Alignment(alignFile.getSeqsAsArray());
alignFile.addAnnotations(al);
al = new Alignment(alignFile.getSeqsAsArray());
alignFile.addAnnotations(al);
+ alignFile.addGroups(al);
+
return al;
} catch (Exception e)
{
return al;
} catch (Exception e)
{