*/
package jalview.gui;
-import java.io.*;
-import java.util.*;
-import java.util.jar.*;
+import jalview.binding.Annotation;
+import jalview.binding.AnnotationElement;
+import jalview.binding.Features;
+import jalview.binding.JGroup;
+import jalview.binding.JSeq;
+import jalview.binding.JalviewModel;
+import jalview.binding.JalviewModelSequence;
+import jalview.binding.Pdbids;
+import jalview.binding.Sequence;
+import jalview.binding.SequenceSet;
+import jalview.binding.Setting;
+import jalview.binding.Tree;
+import jalview.binding.UserColours;
+import jalview.binding.Viewport;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.ResidueProperties;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
+import jalview.util.jarInputStreamProvider;
-import javax.swing.*;
+import java.io.InputStreamReader;
+import java.util.Hashtable;
+import java.util.Vector;
+import java.util.jar.JarEntry;
+import java.util.jar.JarInputStream;
-import org.exolab.castor.xml.*;
+import javax.swing.JOptionPane;
-import jalview.binding.*;
-import jalview.schemes.*;
import jalview.util.MessageManager;
import jalview.util.jarInputStreamProvider;
+import org.exolab.castor.xml.IDResolver;
import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
/**
InputStreamReader in = new InputStreamReader(jin, "UTF-8");
JalviewModel object = new JalviewModel();
- object = (JalviewModel) object.unmarshal(in);
+ object = object.unmarshal(in);
af = LoadFromObject(object, file);
entryCount++;
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Error loading " + file, "Error loading Jalview file",
+ MessageManager.formatMessage("label.error_loading_file_params", new String[]{file}), MessageManager.getString("label.error_loading_jalview_file"),
JOptionPane.WARNING_MESSAGE);
}
});
entry.setId(ids[p].getId());
entry.setType(ids[p].getType());
al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
+ StructureSelectionManager.getStructureSelectionManager(
+ Desktop.instance).registerPDBEntry(entry);
}
}
for (int s = 0; s < ids.length; s++)
{
- seqs.addElement((jalview.datamodel.SequenceI) seqids
+ seqs.addElement(seqids
.elementAt(ids[s]));
}