import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ResidueProperties;
import jalview.structure.StructureMapping;
import jalview.util.MessageManager;
import java.awt.Color;
-import java.io.File;
import java.util.ArrayList;
import java.util.Enumeration;
import java.util.HashMap;
private ChimeraManager viewer;
- /**
+ /*
* set if chimera state is being restored from some source - instructs binding
* not to apply default display style when structure set is updated for first
* time.
*/
private boolean loadingFromArchive = false;
- /**
- * second flag to indicate if the Chimera viewer should ignore sequence
- * colouring events from the structure manager because the GUI is still
- * setting up
+ /*
+ * flag to indicate if the Chimera viewer should ignore sequence colouring
+ * events from the structure manager because the GUI is still setting up
*/
private boolean loadingFinished = true;
- /**
+ /*
* state flag used to check if the Chimera viewer's paint method can be called
*/
private boolean finishedInit = false;
- public boolean isFinishedInit()
- {
- return finishedInit;
- }
-
- public void setFinishedInit(boolean finishedInit)
- {
- this.finishedInit = finishedInit;
- }
-
- boolean allChainsSelected = false;
-
- /**
- * when true, try to search the associated datamodel for sequences that are
- * associated with any unknown structures in the Chimera view.
- */
- private boolean associateNewStructs = false;
+ private List<String> atomsPicked = new ArrayList<String>();
- List<String> atomsPicked = new ArrayList<String>();
-
- public List<String> chainNames;
+ private List<String> chainNames;
private Map<String, String> chainFile;
- StringBuffer eval = new StringBuffer();
+ private StringBuffer eval = new StringBuffer();
public String fileLoadingError;
- private Map<String, List<ChimeraModel>> chimmaps = new LinkedHashMap<String, List<ChimeraModel>>();
-
- private List<String> mdlToFile = new ArrayList<String>();
+ /*
+ * Map of ChimeraModel objects keyed by PDB full local file name
+ */
+ private Map<String, List<ChimeraModel>> chimeraMaps = new LinkedHashMap<String, List<ChimeraModel>>();
- /**
+ /*
* the default or current model displayed if the model cannot be identified
* from the selection message
*/
- int frameNo = 0;
+ private int frameNo = 0;
- String lastCommand;
+ private String lastCommand;
- String lastMessage;
+ private String lastMessage;
- boolean loadedInline;
+ private boolean loadedInline;
+ /**
+ * Open a PDB structure file in Chimera and set up mappings from Jalview.
+ *
+ * We check if the PDB model id is already loaded in Chimera, if so don't
+ * reopen it. This is the case if Chimera has opened a saved session file.
+ *
+ * @param pe
+ * @return
+ */
public boolean openFile(PDBEntry pe)
{
String file = pe.getFile();
try
{
+ List<ChimeraModel> modelsToMap = new ArrayList<ChimeraModel>();
List<ChimeraModel> oldList = viewer.getModelList();
- viewer.openModel(file, pe.getId(), ModelType.PDB_MODEL);
- List<ChimeraModel> newList = viewer.getModelList();
- if (oldList.size() < newList.size())
+ boolean alreadyOpen = false;
+
+ /*
+ * If Chimera already has this model, don't reopen it, but do remap it.
+ */
+ for (ChimeraModel open : oldList)
{
- while (oldList.size() > 0)
+ if (open.getModelName().equals(pe.getId()))
{
- oldList.remove(0);
- newList.remove(0);
- }
- chimmaps.put(file, newList);
- for (ChimeraModel cm : newList)
- {
- while (mdlToFile.size() < 1 + cm.getModelNumber())
- {
- mdlToFile.add(new String(""));
- }
- mdlToFile.set(cm.getModelNumber(), file);
+ alreadyOpen = true;
+ modelsToMap.add(open);
}
+ }
- File fl = new File(file);
- String protocol = AppletFormatAdapter.URL;
- try
- {
- if (fl.exists())
- {
- protocol = AppletFormatAdapter.FILE;
- }
- } catch (Exception e)
- {
- } catch (Error e)
- {
- }
- // Explicitly map to the filename used by Chimera ;
- // pdbentry[pe].getFile(), protocol);
+ /*
+ * If Chimera doesn't yet have this model, ask it to open it, and retrieve
+ * the model names added by Chimera.
+ */
+ if (!alreadyOpen)
+ {
+ viewer.openModel(file, pe.getId(), ModelType.PDB_MODEL);
+ modelsToMap = viewer.getModelList();
+ modelsToMap.removeAll(oldList);
+ }
+
+ chimeraMaps.put(file, modelsToMap);
- if (getSsm() != null)
+ if (getSsm() != null)
+ {
+ getSsm().addStructureViewerListener(this);
+ // ssm.addSelectionListener(this);
+ FeatureRenderer fr = getFeatureRenderer(null);
+ if (fr != null)
{
- getSsm().addStructureViewerListener(this);
- // ssm.addSelectionListener(this);
- FeatureRenderer fr = getFeatureRenderer(null);
- if (fr != null)
- {
- fr.featuresAdded();
- }
- refreshGUI();
+ fr.featuresAdded();
}
- return true;
+ refreshGUI();
}
+ return true;
} catch (Exception q)
{
log("Exception when trying to open model " + file + "\n"
{
if (!viewer.isChimeraLaunched())
{
- viewer.launchChimera(csm.getChimeraPaths());
+ viewer.launchChimera(StructureManager.getChimeraPaths());
}
if (!viewer.isChimeraLaunched())
{
}
/**
- * Send a command to Chimera, and optionally log any responses.
+ * Send a command to Chimera, launching it first if necessary, and optionally
+ * log any responses.
*
* @param command
* @param logResponse
checkLaunched();
if (lastCommand == null || !lastCommand.equals(command))
{
-// Thread t = new Thread(new Runnable()
-// {
-// @Override
-// public void run()
-// {
// trim command or it may never find a match in the replyLog!!
lastReply = viewer.sendChimeraCommand(command.trim(), logResponse);
if (debug && logResponse)
- {
- log("Response from command ('" + command + "') was:\n"
- + lastReply);
- }
-// }
-// });
- // TODO - use j7/8 thread management
-// try
-// {
-// t.join();
-// } catch (InterruptedException foo)
-// {
-// }
-// ;
+ {
+ log("Response from command ('" + command + "') was:\n" + lastReply);
+ }
}
viewerCommandHistory(true);
lastCommand = command;
// // System.arraycopy(mset, 0, modelFileNames, 0, j);
// }
- return chimmaps.keySet().toArray(
- modelFileNames = new String[chimmaps.size()]);
+ return chimeraMaps.keySet().toArray(
+ modelFileNames = new String[chimeraMaps.size()]);
}
/**
public void highlightAtom(int atomIndex, int pdbResNum, String chain,
String pdbfile)
{
- List<ChimeraModel> cms = chimmaps.get(pdbfile);
+ List<ChimeraModel> cms = chimeraMaps.get(pdbfile);
if (cms != null)
{
int mdlNum = cms.get(0).getModelNumber();
return true;
}
+ public boolean isFinishedInit()
+ {
+ return finishedInit;
+ }
+
+ public void setFinishedInit(boolean finishedInit)
+ {
+ this.finishedInit = finishedInit;
+ }
+
+ public List<String> getChainNames()
+ {
+ return chainNames;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff