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Merge branch 'hotfix/JAL-1521' into Release_2_8_2_Branch
[jalview.git]
/
src
/
jalview
/
gui
/
Jalview2XML.java
diff --git
a/src/jalview/gui/Jalview2XML.java
b/src/jalview/gui/Jalview2XML.java
index
8cad9ca
..
105209f
100644
(file)
--- a/
src/jalview/gui/Jalview2XML.java
+++ b/
src/jalview/gui/Jalview2XML.java
@@
-32,6
+32,7
@@
import javax.swing.*;
import org.exolab.castor.xml.*;
import org.exolab.castor.xml.*;
+import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
@@
-39,6
+40,7
@@
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.schemabinding.version2.*;
import jalview.schemes.*;
import jalview.datamodel.SequenceI;
import jalview.schemabinding.version2.*;
import jalview.schemes.*;
+import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.util.jarInputStreamProvider;
import jalview.viewmodel.AlignmentViewport;
import jalview.util.Platform;
import jalview.util.jarInputStreamProvider;
import jalview.viewmodel.AlignmentViewport;
@@
-436,7
+438,7
@@
public class Jalview2XML
for (String dssids : dsses.keySet())
{
AlignFrame _af = dsses.get(dssids);
for (String dssids : dsses.keySet())
{
AlignFrame _af = dsses.get(dssids);
- String jfileName = fileName + " Dataset for " + _af.getTitle();
+ String jfileName = MessageManager.formatMessage("label.dataset_for", new String[]{fileName,_af.getTitle()});
if (!jfileName.endsWith(".xml"))
{
jfileName = jfileName + ".xml";
if (!jfileName.endsWith(".xml"))
{
jfileName = jfileName + ".xml";
@@
-1501,8
+1503,7
@@
public class Jalview2XML
return false;
}
}
return false;
}
}
- throw new Error("Unsupported Version for calcIdparam "
- + calcIdParam.toString());
+ throw new Error(MessageManager.formatMessage("error.unsupported_version_calcIdparam", new String[]{calcIdParam.toString()}));
}
/**
}
/**
@@
-1795,7
+1796,7
@@
public class Jalview2XML
try
{
// create list to store references for any new Jmol viewers created
try
{
// create list to store references for any new Jmol viewers created
- newStructureViewers = new Vector<AppJmol>();
+ newStructureViewers = new Vector<JalviewStructureDisplayI>();
// UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
// Workaround is to make sure caller implements the JarInputStreamProvider
// interface
// UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
// Workaround is to make sure caller implements the JarInputStreamProvider
// interface
@@
-3132,10
+3133,11
@@
public class Jalview2XML
@Override
public void run()
{
@Override
public void run()
{
- AppJmol sview = null;
+ JalviewStructureDisplayI sview = null;
try
{
try
{
- sview = new AppJmol(pdbf, id, sq, alf.alignPanel,
+ // JAL-1333 note - we probably can't migrate Jmol views to UCSF Chimera!
+ sview = new StructureViewer(alf.alignPanel.getStructureSelectionManager()).createView(StructureViewer.Viewer.JMOL, pdbf, id, sq, alf.alignPanel,
useinJmolsuperpos, usetoColourbyseq,
jmolColouring, fileloc, rect, vid);
addNewStructureViewer(sview);
useinJmolsuperpos, usetoColourbyseq,
jmolColouring, fileloc, rect, vid);
addNewStructureViewer(sview);
@@
-3265,13
+3267,13
@@
public class Jalview2XML
return true;
}
return true;
}
- Vector<AppJmol> newStructureViewers = null;
+ Vector<JalviewStructureDisplayI> newStructureViewers = null;
- protected void addNewStructureViewer(AppJmol sview)
+ protected void addNewStructureViewer(JalviewStructureDisplayI sview)
{
if (newStructureViewers != null)
{
{
if (newStructureViewers != null)
{
- sview.jmb.setFinishedLoadingFromArchive(false);
+ sview.getBinding().setFinishedLoadingFromArchive(false);
newStructureViewers.add(sview);
}
}
newStructureViewers.add(sview);
}
}
@@
-3280,9
+3282,9
@@
public class Jalview2XML
{
if (newStructureViewers != null)
{
{
if (newStructureViewers != null)
{
- for (AppJmol sview : newStructureViewers)
+ for (JalviewStructureDisplayI sview : newStructureViewers)
{
{
- sview.jmb.setFinishedLoadingFromArchive(true);
+ sview.getBinding().setFinishedLoadingFromArchive(true);
}
newStructureViewers.clear();
newStructureViewers = null;
}
newStructureViewers.clear();
newStructureViewers = null;