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JAL-3436 null large object reference, tidy method visibility
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Thu, 17 Oct 2019 15:48:06 +0000
(16:48 +0100)
committer
gmungoc
<g.m.carstairs@dundee.ac.uk>
Thu, 17 Oct 2019 15:48:06 +0000
(16:48 +0100)
src/jalview/project/Jalview2XML.java
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diff --git
a/src/jalview/project/Jalview2XML.java
b/src/jalview/project/Jalview2XML.java
index
9507a87
..
b0315e8
100644
(file)
--- a/
src/jalview/project/Jalview2XML.java
+++ b/
src/jalview/project/Jalview2XML.java
@@
-445,7
+445,7
@@
public class Jalview2XML
* @param _jmap
* @return
*/
* @param _jmap
* @return
*/
- public SeqFref newMappingRef(final String sref,
+ protected SeqFref newMappingRef(final String sref,
final jalview.datamodel.Mapping _jmap)
{
SeqFref fref = new SeqFref(sref, "Mapping")
final jalview.datamodel.Mapping _jmap)
{
SeqFref fref = new SeqFref(sref, "Mapping")
@@
-467,7
+467,7
@@
public class Jalview2XML
return fref;
}
return fref;
}
- public SeqFref newAlcodMapRef(final String sref,
+ protected SeqFref newAlcodMapRef(final String sref,
final AlignedCodonFrame _cf,
final jalview.datamodel.Mapping _jmap)
{
final AlignedCodonFrame _cf,
final jalview.datamodel.Mapping _jmap)
{
@@
-499,7
+499,7
@@
public class Jalview2XML
return fref;
}
return fref;
}
- public void resolveFrefedSequences()
+ protected void resolveFrefedSequences()
{
Iterator<SeqFref> nextFref = frefedSequence.iterator();
int toresolve = frefedSequence.size();
{
Iterator<SeqFref> nextFref = frefedSequence.iterator();
int toresolve = frefedSequence.size();
@@
-867,7
+867,7
@@
public class Jalview2XML
* @param out
* jar entry name
*/
* @param out
* jar entry name
*/
- public JalviewModel saveState(AlignmentPanel ap, String fileName,
+ protected JalviewModel saveState(AlignmentPanel ap, String fileName,
JarOutputStream jout, List<String> viewIds)
{
return saveState(ap, fileName, false, jout, viewIds);
JarOutputStream jout, List<String> viewIds)
{
return saveState(ap, fileName, false, jout, viewIds);
@@
-889,7
+889,7
@@
public class Jalview2XML
* @param out
* jar entry name
*/
* @param out
* jar entry name
*/
- public JalviewModel saveState(AlignmentPanel ap, String fileName,
+ protected JalviewModel saveState(AlignmentPanel ap, String fileName,
boolean storeDS, JarOutputStream jout, List<String> viewIds)
{
if (viewIds == null)
boolean storeDS, JarOutputStream jout, List<String> viewIds)
{
if (viewIds == null)
@@
-2798,6
+2798,7
@@
public class Jalview2XML
System.err.println("Error loading alignment: " + x.getMessage());
}
}
System.err.println("Error loading alignment: " + x.getMessage());
}
}
+ this.jarFile = null;
return af;
}
return af;
}
@@
-5632,7
+5633,7
@@
public class Jalview2XML
return false;
}
return false;
}
- public void addToSkipList(AlignFrame af)
+ protected void addToSkipList(AlignFrame af)
{
if (skipList == null)
{
{
if (skipList == null)
{
@@
-5641,7
+5642,7
@@
public class Jalview2XML
skipList.put(af.getViewport().getSequenceSetId(), af);
}
skipList.put(af.getViewport().getSequenceSetId(), af);
}
- public void clearSkipList()
+ protected void clearSkipList()
{
if (skipList != null)
{
{
if (skipList != null)
{
@@
-6126,6
+6127,7
@@
public class Jalview2XML
af.getAlignPanels().clear();
af.closeMenuItem_actionPerformed(true);
af.alignPanel.setHoldRepaint(false);
af.getAlignPanels().clear();
af.closeMenuItem_actionPerformed(true);
af.alignPanel.setHoldRepaint(false);
+ this.jarFile = null;
return af.alignPanel;
}
return af.alignPanel;
}