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JAL-3829 provide both PDBe queries and 3D-Beacons queries in the filter combo box
[jalview.git]
/
src
/
jalview
/
io
/
AlignFile.java
diff --git
a/src/jalview/io/AlignFile.java
b/src/jalview/io/AlignFile.java
index
7b1e84a
..
cea2870
100755
(executable)
--- a/
src/jalview/io/AlignFile.java
+++ b/
src/jalview/io/AlignFile.java
@@
-75,9
+75,9
@@
public abstract class AlignFile extends FileParse
/**
* true if parse() has been called
*/
/**
* true if parse() has been called
*/
- private boolean parseCalled;
+ private boolean parseCalled = false;
- private boolean parseImmediately;
+ private boolean parseImmediately = true;
/**
* @return if doParse() was called at construction time
/**
* @return if doParse() was called at construction time
@@
-112,7
+112,7
@@
public abstract class AlignFile extends FileParse
* @param sourceType
* What type of file to read from (File, URL, Pasted String)
*/
* @param sourceType
* What type of file to read from (File, URL, Pasted String)
*/
- public AlignFile(String dataObject, DataSourceType sourceType)
+ public AlignFile(Object dataObject, DataSourceType sourceType)
throws IOException
{
this(true, dataObject, sourceType);
throws IOException
{
this(true, dataObject, sourceType);
@@
-130,9
+130,10
@@
public abstract class AlignFile extends FileParse
* What type of file to read from (File, URL)
* @throws IOException
*/
* What type of file to read from (File, URL)
* @throws IOException
*/
- public AlignFile(boolean parseImmediately, String dataObject,
+ public AlignFile(boolean parseImmediately, Object dataObject,
DataSourceType sourceType) throws IOException
{
DataSourceType sourceType) throws IOException
{
+ // BH allows File or String
super(dataObject, sourceType);
initData();
if (parseImmediately)
super(dataObject, sourceType);
initData();
if (parseImmediately)