*/
package jalview.ext.jmol;
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Map;
+
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.structure.StructureSelectionManager;
import jalview.util.Comparison;
-import java.awt.Color;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-import java.util.Map;
-
/**
* Routines for generating Jmol commands for Jalview/Jmol binding
*
c.getBlue());
}
-
+ @Deprecated
public String[] colourBySequence(StructureSelectionManager ssm,
String[] files,
SequenceI[][] sequence, SequenceRenderer sr,
public StructureCommandI saveSession(String filepath)
{
/*
- * https://chemapps.stolaf.edu/jmol/docs/#write
- * not currently used in Jalview
+ * https://chemapps.stolaf.edu/jmol/docs/#writemodel
*/
- return new StructureCommand("write \"" + filepath + "\"");
+ return new StructureCommand("write STATE \"" + filepath + "\"");
}
@Override