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JAL-4274 comments to help follow the tests
[jalview.git]
/
src
/
jalview
/
gui
/
AppJmolBinding.java
diff --git
a/src/jalview/gui/AppJmolBinding.java
b/src/jalview/gui/AppJmolBinding.java
index
2699db1
..
158bb54
100644
(file)
--- a/
src/jalview/gui/AppJmolBinding.java
+++ b/
src/jalview/gui/AppJmolBinding.java
@@
-33,8
+33,8
@@
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.datamodel.AlignmentI;
+import jalview.bin.Console;
+import jalview.bin.Jalview;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.ext.jmol.JalviewJmolBinding;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.ext.jmol.JalviewJmolBinding;
@@
-42,9
+42,6
@@
import jalview.io.DataSourceType;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
import jalview.util.Platform;
-import jalview.ws.dbsources.EBIAlfaFold;
-import jalview.ws.dbsources.Pdb;
-import jalview.ws.utils.UrlDownloadClient;
import javajs.util.BS;
public class AppJmolBinding extends JalviewJmolBinding
import javajs.util.BS;
public class AppJmolBinding extends JalviewJmolBinding
@@
-91,7
+88,7
@@
public class AppJmolBinding extends JalviewJmolBinding
jalview.util.BrowserLauncher.openURL(url);
} catch (Exception e)
{
jalview.util.BrowserLauncher.openURL(url);
} catch (Exception e)
{
- Cache.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.
}
}
@@
-156,7
+153,7
@@
public class AppJmolBinding extends JalviewJmolBinding
{
jmolViewer.setJmolCallbackListener(this);
// BH comment: can't do this yet [for JS only, or generally?]
{
jmolViewer.setJmolCallbackListener(this);
// BH comment: can't do this yet [for JS only, or generally?]
- return Platform.isJS() ? null
+ return Platform.isJS() || Jalview.isHeadlessMode() ? null
: new AppConsole(jmolViewer, consolePanel, buttonsToShow);
}
: new AppConsole(jmolViewer, consolePanel, buttonsToShow);
}
@@
-214,7
+211,7
@@
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
+219,7
@@
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
+228,8
@@
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
+239,7
@@
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);