*
* @param command
* Command string to be send.
-- * @param reply
++ * @param getReply
* Flag indicating whether the method should return the reply from
* Chimera or not.
* @return List of Strings corresponding to the lines in the Chimera reply or
* <code>null</code>.
*/
-- public List<String> sendChimeraCommand(String command, boolean reply)
++ public List<String> sendChimeraCommand(String command, boolean getReply)
{
System.out.println("chimeradebug>> " + command);
if (!isChimeraLaunched() || command == null
long startTime = System.currentTimeMillis();
try
{
-- return sendRestCommand(command);
++ return sendRestCommand(command, getReply);
} finally
{
/*
* Sends the command to Chimera's REST API, and returns any response lines.
*
* @param command
++ * @param getReply
* @return
*/
-- protected List<String> sendRestCommand(String command)
++ protected List<String> sendRestCommand(String command, boolean getReply)
{
String restUrl = "http://127.0.0.1:" + this.chimeraRestPort + "/run";
List<NameValuePair> commands = new ArrayList<>(1);
CONNECTION_TIMEOUT_MS, REST_REPLY_TIMEOUT_MS)
: HttpClientUtils.doHttpUrlPost(restUrl, commands,
CONNECTION_TIMEOUT_MS, REST_REPLY_TIMEOUT_MS);
++ if (!getReply)
++ {
++ return null;
++ }
String line = "";
while ((line = response.readLine()) != null)
{
}
@Override
+ public StructureCommandI showStructures(AtomSpecModel restrictTo)
+ {
+ if (restrictTo == null)
+ {
+ return new StructureCommand("display *; cartoon only");
+ }
+ String atomSpec = getAtomSpec(restrictTo, false);
+ String cmd = "display " + atomSpec + "; select displayed; cartoon only";
+ return new StructureCommand(cmd);
+ }
+
+ @Override
+ public StructureCommandI hideChain(String modelId, String chainId)
+ {
+ return new StructureCommand("hide add :" + chainId + "/" + modelId);
+ }
+
+ @Override
+ public StructureCommandI hideAll()
+ {
+ return new StructureCommand("hide *");
+ }
++
+ public StructureCommandI closeViewer()
+ {
+ return null; // not an external viewer
+ }
}
*/
public class PymolCommands extends StructureCommandsBase
{
+ private static final StructureCommand SHOW_RIBBON = new StructureCommand("show", "ribbon");
+
+ private static final StructureCommand SHOW_CARTOON = new StructureCommand("show", "cartoon");
+
+ private static final StructureCommand HIDE_EVERYTHING = new StructureCommand("hide", "everything");
+
- private static final StructureCommand COLOUR_BY_CHAIN = new StructureCommand("spectrum", "chain");
-
- private static final List<StructureCommandI> COLOR_BY_CHARGE = new ArrayList<>();
-
- private static final List<StructureCommandI> SHOW_BACKBONE = new ArrayList<>();
-
- static {
- COLOR_BY_CHARGE.add(new StructureCommand("color", "white", "*"));
- COLOR_BY_CHARGE
- .add(new StructureCommand("color", "red", "resn ASP resn GLU"));
- COLOR_BY_CHARGE.add(
- new StructureCommand("color", "blue", "resn LYS resn ARG"));
- COLOR_BY_CHARGE
- .add(new StructureCommand("color", "yellow", "resn CYS"));
- SHOW_BACKBONE.add(HIDE_EVERYTHING);
- SHOW_BACKBONE.add(SHOW_RIBBON);
- }
+ // https://pymol.org/dokuwiki/doku.php?id=command:zoom
+ // not currently documented on
+ // https://pymolwiki.org/index.php/Category:Commands
+ private static final StructureCommand FOCUS_VIEW = new StructureCommand(
+ "zoom");
+
+ // https://pymolwiki.org/index.php/Quit
+ private static final StructureCommand CLOSE_PYMOL = new StructureCommand(
+ "quit");
+
+ // not currently documented on
+ // https://pymolwiki.org/index.php/Category:Commands
+ private static final StructureCommand COLOUR_BY_CHAIN = new StructureCommand(
+ "spectrum", "chain");
-
+ private static final List<StructureCommandI> COLOR_BY_CHARGE = Arrays
+ .asList(new StructureCommand("color", "white", "*"),
+ new StructureCommand("color", "red", "resn ASP resn GLU"),
+ new StructureCommand("color", "blue",
+ "resn LYS resn ARG"),
+ new StructureCommand("color", "yellow", "resn CYS"));
+
+ private static final List<StructureCommandI> SHOW_BACKBONE = Arrays
+ .asList(new StructureCommand("hide", "everything"),
+ new StructureCommand("show", "ribbon"));
@Override
public StructureCommandI colourByChain()
}
@Override
+ public StructureCommandI showStructures(AtomSpecModel restrictTo)
+ {
+ if (restrictTo == null)
+ {
+ return SHOW_CARTOON;
+ }
+ else
+ {
+ return new StructureCommand("show", "cartoon",
+ getAtomSpec(restrictTo, false));
+ }
+ }
+
+ @Override
+ public StructureCommandI hideChain(String modelId, String chainId)
+ {
+ return new StructureCommand("hide", modelId + "//" + chainId + "//");
+ }
+
+ @Override
+ public StructureCommandI hideAll()
+ {
+ return HIDE_EVERYTHING;
+ }
++
+ public StructureCommandI closeViewer()
+ {
- // https://pymolwiki.org/index.php/Quit
+ return CLOSE_PYMOL;
+ }
}
}
@Override
+ public StructureCommandI showStructures(AtomSpecModel restrictTo)
+ {
+ if (restrictTo == null)
+ {
+ return new StructureCommand("ribbon");
+ }
+
+ String atomSpec = getAtomSpec(restrictTo, false);
+ String cmd = "ribbon " + atomSpec;
+ return new StructureCommand(cmd);
+ }
+
+ @Override
+ public StructureCommandI hideChain(String modelId, String chainId)
+ {
+ String cmd = "~ribbon #" + modelId + ":." + chainId;
+ return new StructureCommand(cmd);
+ }
+
+ @Override
+ public StructureCommandI hideAll()
+ {
+ return new StructureCommand("~display; ~ribbon");
+ }
+ public StructureCommandI closeViewer()
+ {
+ return CLOSE_CHIMERA;
+ }
+
+ @Override
+ public List<StructureCommandI> startNotifications(String uri)
+ {
+ // 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));
+ return cmds;
+ }
+
+ @Override
+ public List<StructureCommandI> stopNotifications()
+ {
+ List<StructureCommandI> cmds = new ArrayList<>();
+ cmds.add(STOP_NOTIFY_MODELS);
+ cmds.add(STOP_NOTIFY_SELECTION);
+ return cmds;
+ }
+
+ @Override
+ public StructureCommandI getSelectedResidues()
+ {
+ return GET_SELECTION;
+ }
+
+ @Override
+ public StructureCommandI listResidueAttributes()
+ {
+ return LIST_RESIDUE_ATTRIBUTES;
+ }
+
+ @Override
+ public StructureCommandI getResidueAttributes(String attName)
+ {
+ // this alternative command
+ // list residues spec ':*/attName' attr attName
+ // doesn't report 'None' values (which is good), but
+ // fails for 'average.bfactor' (which is bad):
+ return new StructureCommand("list residues attr '" + attName + "'");
+ }
}
*/
public class ChimeraXCommands extends ChimeraCommands
{
+ // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/info.html#resattr
- private static final StructureCommand LIST_RESIDUE_ATTRIBUTES = new StructureCommand("info resattr");
++ private static final StructureCommand LIST_RESIDUE_ATTRIBUTES = new StructureCommand(
++ "info resattr");
+
+ // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/exit.html
- private static final StructureCommand CLOSE_CHIMERAX = new StructureCommand("exit");
++ private static final StructureCommand CLOSE_CHIMERAX = new StructureCommand(
++ "exit");
+
+ // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/info.html#notify
- private static final StructureCommand STOP_NOTIFY_SELECTION = new StructureCommand("info notify stop selection jalview");
++ private static final StructureCommand STOP_NOTIFY_SELECTION = new StructureCommand(
++ "info notify stop selection jalview");
+
- private static final StructureCommand STOP_NOTIFY_MODELS = new StructureCommand("info notify stop models jalview");
++ private static final StructureCommand STOP_NOTIFY_MODELS = new StructureCommand(
++ "info notify stop models jalview");
+
+ // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/info.html#selection
+ private static final StructureCommand GET_SELECTION = new StructureCommand(
+ "info selection level residue");
+
private static final StructureCommand SHOW_BACKBONE = new StructureCommand(
"~display all;~ribbon;show @CA|P atoms");
}
@Override
+ public StructureCommandI hideChain(String modelId, String chainId)
+ {
+ String cmd = "~ribbon #" + modelId + "/" + chainId;
+ return new StructureCommand(cmd);
+ }
++
+ public StructureCommandI closeViewer()
+ {
+ return CLOSE_CHIMERAX;
+ }
+
+ @Override
+ public List<StructureCommandI> startNotifications(String uri)
+ {
+ List<StructureCommandI> cmds = new ArrayList<>();
- cmds.add(new StructureCommand("info notify start models prefix ModelChanged jalview url " + uri));
- cmds.add(new StructureCommand("info notify start selection jalview prefix SelectionChanged url " + uri));
++ cmds.add(new StructureCommand(
++ "info notify start models prefix ModelChanged jalview url "
++ + uri));
++ cmds.add(new StructureCommand(
++ "info notify start selection jalview prefix SelectionChanged url "
++ + uri));
+ return cmds;
+ }
+
+ @Override
+ public List<StructureCommandI> stopNotifications()
+ {
+ List<StructureCommandI> cmds = new ArrayList<>();
+ cmds.add(STOP_NOTIFY_MODELS);
+ cmds.add(STOP_NOTIFY_SELECTION);
+ return cmds;
+ }
+
+ @Override
+ public StructureCommandI getSelectedResidues()
+ {
+ return GET_SELECTION;
+ }
+
+ @Override
+ public StructureCommandI listResidueAttributes()
+ {
+ return LIST_RESIDUE_ATTRIBUTES;
+ }
}
StructureCommandI openSession(String filepath);
/**
+ * Returns a command to show structures in the viewer. If {@code restrictTo}
+ * is null, all structures are included, otherwise the display is restricted
+ * to positions represented in the model
+ *
+ * @param restrictTo
+ * @return
+ */
+ StructureCommandI showStructures(AtomSpecModel restrictTo);
+
+ /**
+ * Returns a command to hide the specified model chain in the structure viewer
+ *
+ * @param modelId
+ * @param chainId
+ * @return
+ */
+ StructureCommandI hideChain(String modelId, String chainId);
+
+ /**
+ * Returns a command to hide everything in the structure viewer
+ *
+ * @return
+ */
+ StructureCommandI hideAll();
++
++ /**
+ * Returns a command to ask the viewer to close down
+ *
+ * @return
+ */
+ StructureCommandI closeViewer();
+
+ /**
+ * Returns one or more commands to ask the viewer to notify model or selection
+ * changes to the given uri. Returns null if this is not supported by the
+ * structure viewer.
+ *
+ * @param uri
+ * @return
+ */
+ List<StructureCommandI> startNotifications(String uri);
+
+ /**
+ * Returns one or more commands to ask the viewer to stop notifying model or
+ * selection changes. Returns null if this is not supported by the structure
+ * viewer.
+ *
+ * @return
+ */
+ List<StructureCommandI> stopNotifications();
+
+ /**
+ * Returns a command to ask the viewer for its current residue selection, or
+ * null if no such command is supported
+ *
+ * @return
+ */
+ StructureCommandI getSelectedResidues();
+
+ /**
+ * Returns a command to list the unique names of residue attributes, or null
+ * if no such command is supported
+ *
+ * @return
+ */
+ StructureCommandI listResidueAttributes();
+
+ /**
+ * Returns a command to list residues with an attribute of the given name,
+ * with attribute value, or null if no such command is supported
+ *
+ * @return
+ */
+ StructureCommandI getResidueAttributes(String attName);
}
public String fileLoadingError;
+ private boolean showAlignmentOnly;
+
+ /*
+ * a list of chains "pdbid:chainid" to hide in the viewer
+ */
+ // TODO make private once deprecated JalviewJmolBinding.centerViewer removed
+ protected List<String> chainsToHide;
+
+ private boolean hideHiddenRegions;
+
+ protected Thread externalViewerMonitor;
+
/**
* Constructor
*
private List<String> executeCommand(StructureCommandI cmd,
boolean getReply, String msg)
{
+ if (cmd == null)
+ {
+ return null; // catch unimplemented commands
+ }
+ final JalviewStructureDisplayI theViewer = getViewer();
+ final long handle = msg == null ? 0 : theViewer.startProgressBar(msg);
if (getReply)
{
/*
}
@Test(groups = "Functional")
+ public void testHideAll()
+ {
+ StructureCommandI cmd = testee.hideAll();
+ assertEquals(cmd, new StructureCommand("hide", "everything"));
+ }
+
+ @Test(groups = "Functional")
+ public void testHideChain()
+ {
+ StructureCommandI cmd = testee.hideChain("1.1", "B");
+ assertEquals(cmd, new StructureCommand("hide", "1.1//B//"));
+ }
+
+ @Test(groups = "Functional")
+ public void testShowStructures()
+ {
+ /*
+ * with nothing excluded
+ */
+ StructureCommandI cmd = testee.showStructures(null);
+ assertEquals(cmd, new StructureCommand("show", "cartoon"));
+
+ /*
+ * restricted to specified positions
+ */
+ AtomSpecModel restrictTo = new AtomSpecModel();
+ restrictTo.addRange("1.1", 12, 20, "A");
+ restrictTo.addRange("1.1", 30, 35, "A");
+ restrictTo.addRange("2.1", 11, 30, "B");
+ cmd = testee.showStructures(restrictTo);
+ assertEquals(cmd, new StructureCommand("show", "cartoon",
+ "1.1//A/12-20+30-35/ 2.1//B/11-30/"));
+ }
++
+ public void testCloseViewer()
+ {
+ assertEquals(testee.closeViewer(), new StructureCommand("quit"));
+ }
}
}
@Test(groups = "Functional")
+ public void testHideAll()
+ {
+ StructureCommandI cmd = testee.hideAll();
- assertEquals(cmd.getCommand(), "~display all; ~ribbon");
++ assertEquals(cmd.getCommand(), "~display; ~ribbon");
+ }
+
+ @Test(groups = "Functional")
+ public void testHideChain()
+ {
+ StructureCommandI cmd = testee.hideChain("1.1", "B");
+ assertEquals(cmd.getCommand(), "~ribbon #1.1:.B");
+ }
+
+ @Test(groups = "Functional")
+ public void testShowStructures()
+ {
+ /*
+ * with nothing excluded
+ */
+ StructureCommandI cmd = testee.showStructures(null);
+ assertEquals(cmd.getCommand(), "ribbon");
+
+ /*
+ * restricted to specified positions
+ */
+ AtomSpecModel restrictTo = new AtomSpecModel();
+ restrictTo.addRange("1.1", 12, 20, "A");
+ restrictTo.addRange("1.1", 30, 35, "A");
+ restrictTo.addRange("2.1", 11, 30, "B");
+ cmd = testee.showStructures(restrictTo);
+ assertEquals(cmd.getCommand(),
+ "ribbon #1.1:12-20.A,30-35.A|#2.1:11-30.B");
+ }
++
+ public void testCloseViewer()
+ {
+ assertEquals(testee.closeViewer(), new StructureCommand("stop really"));
+ }
+
+ @Test(groups = "Functional")
+ public void testGetSelectedResidues()
+ {
+ assertEquals(testee.getSelectedResidues(),
+ new StructureCommand("list selection level residue"));
+ }
+
+ @Test(groups = "Functional")
+ public void testListResidueAttributes()
+ {
+ assertEquals(testee.listResidueAttributes(),
+ new StructureCommand("list resattr"));
+ }
+
+ @Test(groups = "Functional")
+ public void testGetResidueAttributes()
+ {
+ assertEquals(testee.getResidueAttributes("binding site"),
+ new StructureCommand("list residues attr 'binding site'"));
+ }
+
+ @Test(groups = "Functional")
+ public void testStartNotifications()
+ {
+ List<StructureCommandI> cmds = testee.startNotifications("to here");
+ assertEquals(cmds.size(), 2);
+ assertEquals(cmds.get(0), new StructureCommand("listen start models url to here"));
+ assertEquals(cmds.get(1), new StructureCommand("listen start select prefix SelectionChanged url to here"));
+ }
+
+ @Test(groups = "Functional")
+ public void testStopNotifications()
+ {
+ List<StructureCommandI> cmds = testee.stopNotifications();
+ assertEquals(cmds.size(), 2);
+ assertEquals(cmds.get(0), new StructureCommand("listen stop models"));
+ assertEquals(cmds.get(1), new StructureCommand("listen stop selection"));
+ }
}
}
@Test(groups = "Functional")
+ public void testHideAll()
+ {
+ StructureCommandI cmd = testee.hideAll();
- assertEquals(cmd.getCommand(), "~display all; ~ribbon");
++ assertEquals(cmd.getCommand(), "~display; ~ribbon");
+ }
+
+ @Test(groups = "Functional")
+ public void testHideChain()
+ {
+ StructureCommandI cmd = testee.hideChain("1.1", "B");
+ assertEquals(cmd.getCommand(), "~ribbon #1.1/B");
+ }
+
+ @Test(groups = "Functional")
+ public void testShowStructures()
+ {
+ /*
+ * with nothing excluded
+ */
+ StructureCommandI cmd = testee.showStructures(null);
+ assertEquals(cmd.getCommand(), "ribbon");
+
+ /*
+ * restricted to specified positions
+ */
+ AtomSpecModel restrictTo = new AtomSpecModel();
+ restrictTo.addRange("1.1", 12, 20, "A");
+ restrictTo.addRange("1.1", 30, 35, "A");
+ restrictTo.addRange("2.1", 11, 30, "B");
+ cmd = testee.showStructures(restrictTo);
+ assertEquals(cmd.getCommand(),
+ "ribbon #1.1/A:12-20,30-35|#2.1/B:11-30");
+ }
++
+ public void testCloseViewer()
+ {
+ assertEquals(testee.closeViewer(), new StructureCommand("exit"));
+ }
+
+ @Test(groups = "Functional")
+ public void testGetSelectedResidues()
+ {
+ assertEquals(testee.getSelectedResidues(),
+ new StructureCommand("info selection level residue"));
+ }
+
+ @Test(groups = "Functional")
+ public void testStartNotifications()
+ {
+ List<StructureCommandI> cmds = testee.startNotifications("to here");
+ assertEquals(cmds.size(), 2);
+ assertEquals(cmds.get(0), new StructureCommand("info notify start models prefix ModelChanged jalview url to here"));
+ assertEquals(cmds.get(1), new StructureCommand("info notify start selection jalview prefix SelectionChanged url to here"));
+ }
+
+ @Test(groups = "Functional")
+ public void testStopNotifications()
+ {
+ List<StructureCommandI> cmds = testee.stopNotifications();
+ assertEquals(cmds.size(), 2);
+ assertEquals(cmds.get(0), new StructureCommand("info notify stop models jalview"));
+ assertEquals(cmds.get(1), new StructureCommand("info notify stop selection jalview"));
+ }
+
+ @Test(groups = "Functional")
+ public void testListResidueAttributes()
+ {
+ assertEquals(testee.listResidueAttributes(),
+ new StructureCommand("info resattr"));
+ }
}
git://source.jalview.org / jalview.git / commitdiff