*/
package jalview.ext.rbvi.chimera;
-import java.util.Locale;
-
import java.awt.Color;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
import jalview.structure.AtomSpecModel;
import jalview.structure.StructureCommand;
import jalview.structure.StructureCommandI;
import jalview.structure.StructureCommandsBase;
-import jalview.structure.StructureCommandsI.AtomSpecType;
import jalview.util.ColorUtils;
/**
public class ChimeraCommands extends StructureCommandsBase
{
// https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/focus.html
- private static final StructureCommand FOCUS_VIEW = new StructureCommand("focus");
+ private static final StructureCommand FOCUS_VIEW = new StructureCommand(
+ "focus");
// https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html#listresattr
- private static final StructureCommand LIST_RESIDUE_ATTRIBUTES = new StructureCommand("list resattr");
+ private static final StructureCommand LIST_RESIDUE_ATTRIBUTES = new StructureCommand(
+ "list resattr");
// https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/stop.html
- private static final StructureCommand CLOSE_CHIMERA = new StructureCommand("stop really");
+ private static final StructureCommand CLOSE_CHIMERA = new StructureCommand(
+ "stop really");
// https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html
- private static final StructureCommand STOP_NOTIFY_SELECTION = new StructureCommand("listen stop selection");
+ private static final StructureCommand STOP_NOTIFY_SELECTION = new StructureCommand(
+ "listen stop selection");
- private static final StructureCommand STOP_NOTIFY_MODELS = new StructureCommand("listen stop models");
+ private static final StructureCommand STOP_NOTIFY_MODELS = new StructureCommand(
+ "listen stop models");
// https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html#listselection
- private static final StructureCommand GET_SELECTION = new StructureCommand("list selection level residue");
+ private static final StructureCommand GET_SELECTION = new StructureCommand(
+ "list selection level residue");
private static final StructureCommand SHOW_BACKBONE = new StructureCommand(
"~display all;~ribbon;chain @CA|P");
* @return
*/
protected StructureCommandI setAttribute(String attributeName,
- String attributeValue,
- AtomSpecModel atomSpecModel)
+ String attributeValue, AtomSpecModel atomSpecModel)
{
StringBuilder sb = new StringBuilder(128);
sb.append("setattr res ").append(attributeName).append(" '")
StringBuilder cmd = new StringBuilder();
String atomSpecAlphaOnly = getAtomSpec(spec, backbone);
String refSpecAlphaOnly = getAtomSpec(ref, backbone);
- cmd.append("match ").append(atomSpecAlphaOnly).append(" ").append(refSpecAlphaOnly);
+ cmd.append("match ").append(atomSpecAlphaOnly).append(" ")
+ .append(refSpecAlphaOnly);
/*
* show superposed residues as ribbon
// https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html
List<StructureCommandI> cmds = new ArrayList<>();
cmds.add(new StructureCommand("listen start models url " + uri));
- cmds.add(new StructureCommand("listen start select prefix SelectionChanged url " + uri));
+ cmds.add(new StructureCommand(
+ "listen start select prefix SelectionChanged url " + uri));
return cmds;
}
return new StructureCommand("list residues attr '" + attName + "'");
}
+ @Override
+ public List<StructureCommandI> centerViewOn(List<AtomSpecModel> residues)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
}