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JAL-653 (experimental) 'realise' dummy sequences in add alignment
[jalview.git]
/
src
/
jalview
/
io
/
packed
/
ParsePackedSet.java
diff --git
a/src/jalview/io/packed/ParsePackedSet.java
b/src/jalview/io/packed/ParsePackedSet.java
index
df1acf1
..
01369b9
100644
(file)
--- a/
src/jalview/io/packed/ParsePackedSet.java
+++ b/
src/jalview/io/packed/ParsePackedSet.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.
*
@@
-30,7
+30,7
@@
import jalview.io.packed.DataProvider.JvDataType;
import java.io.BufferedReader;
import java.io.IOException;
import java.util.ArrayList;
import java.io.BufferedReader;
import java.io.IOException;
import java.util.ArrayList;
-import java.util.Hashtable;
+import java.util.HashMap;
import java.util.List;
public class ParsePackedSet
import java.util.List;
public class ParsePackedSet
@@
-66,7
+66,7
@@
public class ParsePackedSet
String fmt = null;
try
{
String fmt = null;
try
{
- fmt = new IdentifyFile().Identify(src, false);
+ fmt = new IdentifyFile().identify(src, false);
} catch (Exception ex)
{
exerror = ex;
} catch (Exception ex)
{
exerror = ex;
@@
-123,8
+123,9
@@
public class ParsePackedSet
{
br = new BufferedReader(src.getReader());
}
{
br = new BufferedReader(src.getReader());
}
+ // TODO: add columnSelection to context
if (new jalview.io.AnnotationFile().parseAnnotationFrom(
if (new jalview.io.AnnotationFile().parseAnnotationFrom(
- context.getLastAlignment(), br))
+ context.getLastAlignment(), null, br))
{
context.updateSetModified(true);
}
{
context.updateSetModified(true);
}
@@
-156,7
+157,7
@@
public class ParsePackedSet
// if not, create one.
if (context.featureColours == null)
{
// if not, create one.
if (context.featureColours == null)
{
- context.featureColours = new Hashtable();
+ context.featureColours = new HashMap<String, Object>();
}
try
{
}
try
{