From 6b74ef88014ba574bd60a14eae8167390e012421 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Thu, 17 Oct 2019 16:48:06 +0100 Subject: [PATCH] JAL-3436 null large object reference, tidy method visibility --- src/jalview/project/Jalview2XML.java | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java index 9507a87..b0315e8 100644 --- a/src/jalview/project/Jalview2XML.java +++ b/src/jalview/project/Jalview2XML.java @@ -445,7 +445,7 @@ public class Jalview2XML * @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") @@ -467,7 +467,7 @@ public class Jalview2XML return fref; } - public SeqFref newAlcodMapRef(final String sref, + protected SeqFref newAlcodMapRef(final String sref, final AlignedCodonFrame _cf, final jalview.datamodel.Mapping _jmap) { @@ -499,7 +499,7 @@ public class Jalview2XML return fref; } - public void resolveFrefedSequences() + protected void resolveFrefedSequences() { Iterator nextFref = frefedSequence.iterator(); int toresolve = frefedSequence.size(); @@ -867,7 +867,7 @@ public class Jalview2XML * @param out * jar entry name */ - public JalviewModel saveState(AlignmentPanel ap, String fileName, + protected JalviewModel saveState(AlignmentPanel ap, String fileName, JarOutputStream jout, List viewIds) { return saveState(ap, fileName, false, jout, viewIds); @@ -889,7 +889,7 @@ public class Jalview2XML * @param out * jar entry name */ - public JalviewModel saveState(AlignmentPanel ap, String fileName, + protected JalviewModel saveState(AlignmentPanel ap, String fileName, boolean storeDS, JarOutputStream jout, List viewIds) { if (viewIds == null) @@ -2798,6 +2798,7 @@ public class Jalview2XML System.err.println("Error loading alignment: " + x.getMessage()); } } + this.jarFile = null; return af; } @@ -5632,7 +5633,7 @@ public class Jalview2XML return false; } - public void addToSkipList(AlignFrame af) + protected void addToSkipList(AlignFrame af) { if (skipList == null) { @@ -5641,7 +5642,7 @@ public class Jalview2XML skipList.put(af.getViewport().getSequenceSetId(), af); } - public void clearSkipList() + protected void clearSkipList() { if (skipList != null) { @@ -6126,6 +6127,7 @@ public class Jalview2XML af.getAlignPanels().clear(); af.closeMenuItem_actionPerformed(true); af.alignPanel.setHoldRepaint(false); + this.jarFile = null; return af.alignPanel; } -- 1.7.10.2