import jalview.api.FeatureRenderer;\r
import jalview.api.SequenceRenderer;\r
import jalview.api.SequenceStructureBinding;\r
+import jalview.api.StructureSelectionManagerProvider;\r
import jalview.datamodel.*;\r
import jalview.structure.*;\r
import jalview.io.*;\r
\r
public abstract class JalviewJmolBinding implements StructureListener,\r
JmolStatusListener, SequenceStructureBinding,\r
- JmolSelectionListener, ComponentListener\r
+ JmolSelectionListener, ComponentListener, StructureSelectionManagerProvider\r
\r
{\r
/**\r
*/\r
public SequenceI[][] sequence;\r
\r
- StructureSelectionManager ssm;\r
+ public StructureSelectionManager ssm;\r
\r
public JmolViewer viewer;\r
\r
- public JalviewJmolBinding(PDBEntry[] pdbentry, SequenceI[][] sequenceIs,\r
+ public JalviewJmolBinding(StructureSelectionManager ssm, PDBEntry[] pdbentry, SequenceI[][] sequenceIs,\r
String[][] chains, String protocol)\r
{\r
+ this.ssm = ssm;\r
this.sequence = sequenceIs;\r
this.chains = chains;\r
this.pdbentry = pdbentry;\r
*/\r
}\r
\r
- public JalviewJmolBinding(JmolViewer viewer2)\r
+ public JalviewJmolBinding(StructureSelectionManager ssm, JmolViewer viewer2)\r
{\r
+ this.ssm = ssm;\r
viewer = viewer2;\r
viewer.setJmolStatusListener(this);\r
viewer.addSelectionListener(this);\r
{\r
viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE);\r
// remove listeners for all structures in viewer\r
- StructureSelectionManager.getStructureSelectionManager()\r
- .removeStructureViewerListener(this, this.getPdbFile());\r
+ ssm.removeStructureViewerListener(this, this.getPdbFile());\r
// and shut down jmol\r
viewer.evalStringQuiet("zap");\r
viewer.setJmolStatusListener(null);\r
chainFile = new Hashtable();\r
boolean notifyLoaded = false;\r
String[] modelfilenames = getPdbFile();\r
- ssm = StructureSelectionManager.getStructureSelectionManager();\r
// first check if we've lost any structures\r
if (oldmodels != null && oldmodels.length > 0)\r
{\r
chains[pe] = null;\r
}\r
}\r
+ /**\r
+ * \r
+ * @param pdbfile\r
+ * @return text report of alignment between pdbfile and any associated alignment sequences\r
+ */\r
+ public String printMapping(String pdbfile)\r
+ {\r
+ return ssm.printMapping(pdbfile);\r
+ }\r
+\r
}\r