-
- /*
- * Broadcast the selection (which may be empty, if the user just cleared all
- * selections)
- */
- getSsm().mouseOverStructure(atomSpecs);
- }
-
- private void log(String message)
- {
- System.err.println("## Chimera log: " + message);
- }
-
- private void viewerCommandHistory(boolean enable)
- {
- // log("(Not yet implemented) History "
- // + ((debug || enable) ? "on" : "off"));
- }
-
- public long getLoadNotifiesHandled()
- {
- return loadNotifiesHandled;
- }
-
- public void setJalviewColourScheme(ColourSchemeI cs)
- {
- colourBySequence = false;
-
- if (cs == null)
- {
- return;
- }
-
- // Chimera expects RBG values in the range 0-1
- final double normalise = 255D;
- viewerCommandHistory(false);
- StringBuilder command = new StringBuilder(128);
-
- List<String> residueSet = ResidueProperties.getResidues(isNucleotide(),
- false);
- for (String res : residueSet)
- {
- Color col = cs.findColour(res.charAt(0));
- command.append("color " + col.getRed() / normalise + ","
- + col.getGreen() / normalise + "," + col.getBlue()
- / normalise + " ::" + res + ";");
- }
-
- evalStateCommand(command.toString(),false);
- viewerCommandHistory(true);
- }
-
- /**
- * called when the binding thinks the UI needs to be refreshed after a Chimera
- * state change. this could be because structures were loaded, or because an
- * error has occurred.
- */
- public abstract void refreshGUI();
-
- public void setLoadingFromArchive(boolean loadingFromArchive)
- {
- this.loadingFromArchive = loadingFromArchive;
- }
-
- /**
- *
- * @return true if Chimeral is still restoring state or loading is still going
- * on (see setFinsihedLoadingFromArchive)
- */
- public boolean isLoadingFromArchive()
- {
- return loadingFromArchive && !loadingFinished;
- }
-
- /**
- * modify flag which controls if sequence colouring events are honoured by the
- * binding. Should be true for normal operation
- *
- * @param finishedLoading
- */
- public void setFinishedLoadingFromArchive(boolean finishedLoading)
- {
- loadingFinished = finishedLoading;