X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fpymol%2FPymolCommands.java;h=e4f9f5f8d27911efec4a26791c70e98e05898071;hb=27f24d1f14b8e8704d72797286f7a6e5f60b2119;hp=910aae1d69eef0428c7299519946eb95f432ff8b;hpb=8c29d4d93761896bb75c6c3b24c3fdd0612c7bb3;p=jalview.git diff --git a/src/jalview/ext/pymol/PymolCommands.java b/src/jalview/ext/pymol/PymolCommands.java index 910aae1..e4f9f5f 100644 --- a/src/jalview/ext/pymol/PymolCommands.java +++ b/src/jalview/ext/pymol/PymolCommands.java @@ -1,14 +1,15 @@ package jalview.ext.pymol; +import java.awt.Color; +import java.util.ArrayList; +import java.util.List; +import java.util.Map; + import jalview.structure.AtomSpecModel; import jalview.structure.StructureCommand; import jalview.structure.StructureCommandI; import jalview.structure.StructureCommandsBase; -import java.awt.Color; -import java.util.ArrayList; -import java.util.List; - /** * A class that generates commands to send to PyMol over its XML-RPC interface. *
@@ -119,9 +120,8 @@ public class PymolCommands extends StructureCommandsBase
@Override
public StructureCommandI openCommandFile(String path)
{
- // where is this documented by PyMol?
- // todo : xml-rpc answers 'method "@" is not supported'
- return new StructureCommand("@" + path); // should be .pml
+ // https://pymolwiki.org/index.php/Run
+ return new StructureCommand("run", path); // should be .pml
}
@Override
@@ -210,4 +210,27 @@ public class PymolCommands extends StructureCommandsBase
return new StructureCommand("load", file);
}
+ /**
+ * Overrides the default implementation (which generates concatenated
+ * commands) to generate one per colour (because the XML-RPC interface to
+ * PyMOL only accepts one command at a time)
+ *
+ * @param colourMap
+ * @return
+ */
+ @Override
+ public List