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Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges
[jalview.git]
/
src
/
jalview
/
gui
/
AppJmolBinding.java
diff --git
a/src/jalview/gui/AppJmolBinding.java
b/src/jalview/gui/AppJmolBinding.java
index
6b06e56
..
844faa7
100644
(file)
--- a/
src/jalview/gui/AppJmolBinding.java
+++ b/
src/jalview/gui/AppJmolBinding.java
@@
-33,7
+33,7
@@
import org.openscience.jmol.app.jmolpanel.console.AppConsole;
import jalview.api.AlignmentViewPanel;
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.api.AlignmentViewPanel;
import jalview.api.structures.JalviewStructureDisplayI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
@@
-91,7
+91,7
@@
public class AppJmolBinding extends JalviewJmolBinding
jalview.util.BrowserLauncher.openURL(url);
} catch (Exception e)
{
jalview.util.BrowserLauncher.openURL(url);
} catch (Exception e)
{
- Cache.log.error("Failed to launch Jmol-associated url " + url, e);
+ Console.error("Failed to launch Jmol-associated url " + url, e);
// TODO: 2.6 : warn user if browser was not configured.
}
}
// TODO: 2.6 : warn user if browser was not configured.
}
}
@@
-214,7
+214,7
@@
public class AppJmolBinding extends JalviewJmolBinding
{
// todo - record which pdbids were successfully imported.
StringBuilder errormsgs = new StringBuilder();
{
// todo - record which pdbids were successfully imported.
StringBuilder errormsgs = new StringBuilder();
-
+
List<String> files = new ArrayList<>();
String pdbid = "";
try
List<String> files = new ArrayList<>();
String pdbid = "";
try
@@
-222,7
+222,7
@@
public class AppJmolBinding extends JalviewJmolBinding
String[] filesInViewer = getStructureFiles();
// TODO: replace with reference fetching/transfer code (validate PDBentry
// as a DBRef?)
String[] filesInViewer = getStructureFiles();
// TODO: replace with reference fetching/transfer code (validate PDBentry
// as a DBRef?)
-
+
for (int pi = 0; pi < getPdbCount(); pi++)
{
PDBEntry strucEntry = getPdbEntry(pi);
for (int pi = 0; pi < getPdbCount(); pi++)
{
PDBEntry strucEntry = getPdbEntry(pi);
@@
-231,7
+231,8
@@
public class AppJmolBinding extends JalviewJmolBinding
if (file == null)
{
pdbid = strucEntry.getId();
if (file == null)
{
pdbid = strucEntry.getId();
- try{
+ try
+ {
file = structureViewer.fetchPdbFile(strucEntry);
} catch (OutOfMemoryError oomerror)
{
file = structureViewer.fetchPdbFile(strucEntry);
} catch (OutOfMemoryError oomerror)
{
@@
-241,7
+242,7
@@
public class AppJmolBinding extends JalviewJmolBinding
ex.printStackTrace();
errormsgs.append("'").append(pdbid).append("'");
}
ex.printStackTrace();
errormsgs.append("'").append(pdbid).append("'");
}
- if (file!=null)
+ if (file != null)
{
// success
files.add(file);
{
// success
files.add(file);
@@
-282,7
+283,7
@@
public class AppJmolBinding extends JalviewJmolBinding
}
if (errormsgs.length() > 0)
{
}
if (errormsgs.length() > 0)
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getInstance(),
MessageManager.formatMessage(
"label.pdb_entries_couldnt_be_retrieved", new String[]
{ errormsgs.toString() }),
MessageManager.formatMessage(
"label.pdb_entries_couldnt_be_retrieved", new String[]
{ errormsgs.toString() }),