package jalview.io;
import jalview.bin.Cache;
+import jalview.bin.Instance;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.GraphLine;
import jalview.io.vamsas.DatastoreItem;
import jalview.io.vamsas.DatastoreRegistry;
import jalview.io.vamsas.Rangetype;
+import jalview.project.Jalview2XML;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
// /SAVE THE TREES
// /////////////////////////////////
// FIND ANY ASSOCIATED TREES
- if (Desktop.desktop != null)
+ if (Desktop.getDesktopPane() != null)
{
- javax.swing.JInternalFrame[] frames = Desktop.instance
+ javax.swing.JInternalFrame[] frames = Instance.getDesktop()
.getAllFrames();
for (int t = 0; t < frames.length; t++)
// client data is shared over all app clients
try
{
- jalview.gui.Jalview2XML fromxml = new jalview.gui.Jalview2XML();
+ // jalview.gui.Jalview2XML fromxml = new jalview.gui.Jalview2XML();
+ Jalview2XML fromxml = new Jalview2XML();
fromxml.attemptversion1parse = false;
fromxml.setUniqueSetSuffix("");
fromxml.setObjectMappingTables(vobj2jv, jv2vobj); // mapKeysToString
// user data overrides data shared over all app clients ?
try
{
- jalview.gui.Jalview2XML fromxml = new jalview.gui.Jalview2XML();
+ Jalview2XML fromxml = new Jalview2XML();
fromxml.attemptversion1parse = false;
fromxml.setUniqueSetSuffix("");
fromxml.setSkipList(skipList);
if (mappings != null)
{
jalview.structure.StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance)
+ .getStructureSelectionManager(Instance.getDesktop())
.registerMappings(mappings);
}
}
{
try
{
- jalview.gui.Jalview2XML jxml = new jalview.gui.Jalview2XML();
+ Jalview2XML jxml = new Jalview2XML();
jxml.setObjectMappingTables(mapKeysToString(vobj2jv),
mapValuesToString(jv2vobj));
jxml.setSkipList(skipList);
}
// bitfields - should be a template in j1.5
- private static int HASSECSTR = 0;
+ private static final int HASSECSTR = 0;
- private static int HASVALS = 1;
+ private static final int HASVALS = 1;
- private static int HASHPHOB = 2;
+ private static final int HASHPHOB = 2;
- private static int HASDC = 3;
+ private static final int HASDC = 3;
- private static int HASDESCSTR = 4;
+ private static final int HASDESCSTR = 4;
- private static int HASTWOSTATE = 5; // not used yet.
+ private static final int HASTWOSTATE = 5; // not used yet.
/**
* parses the AnnotationElements - if they exist - into