import java.awt.Color;
import java.net.BindException;
import java.util.ArrayList;
+import java.util.Hashtable;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
private static final String ALPHACARBON = "CA";
+ private List<String> chainNames = new ArrayList<String>();
+
+ private Hashtable<String, String> chainFile = new Hashtable<String, String>();
/*
* Object through which we talk to Chimera
*/
private String lastCommand;
- private boolean loadedInline;
-
- /**
- * current set of model filenames loaded
- */
- String[] modelFileNames = null;
-
- String lastMousedOverAtomSpec;
-
- private List<String> lastReply;
+ String lastHighlightCommand;
/*
* incremented every time a load notification is successfully handled -
* @param protocol
*/
public JalviewChimeraBinding(StructureSelectionManager ssm,
- PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
- String protocol)
+ PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String protocol)
{
- super(ssm, pdbentry, sequenceIs, chains, protocol);
+ super(ssm, pdbentry, sequenceIs, protocol);
viewer = new ChimeraManager(
new ext.edu.ucsf.rbvi.strucviz2.StructureManager(true));
}
boolean first = true;
for (String chain : toshow)
{
+ int modelNumber = getModelNoForChain(chain);
+ String showChainCmd = modelNumber == -1 ? "" : modelNumber + ":."
+ + chain.split(":")[1];
if (!first)
{
cmd.append(",");
}
- cmd.append(":.").append(chain);
+ cmd.append(showChainCmd);
first = false;
}
* window, but it looks more helpful not to (easier to relate chains to the
* whole)
*/
- final String command = "~display #*; ~ribbon #*; ribbon "
+ final String command = "~display #*; ~ribbon #*; ribbon :"
+ cmd.toString();
sendChimeraCommand(command, false);
}
if (lastCommand == null || !lastCommand.equals(command))
{
// trim command or it may never find a match in the replyLog!!
- lastReply = viewer.sendChimeraCommand(command.trim(), logResponse);
+ List<String> lastReply = viewer.sendChimeraCommand(command.trim(),
+ logResponse);
if (logResponse && debug)
{
log("Response from command ('" + command + "') was:\n" + lastReply);
// End StructureListener
// //////////////////////////
- public Color getColour(int atomIndex, int pdbResNum, String chain,
- String pdbfile)
- {
- if (getModelNum(pdbfile) < 0)
- {
- return null;
- }
- log("get model / residue colour attribute unimplemented");
- return null;
- }
-
/**
* returns the current featureRenderer that should be used to colour the
* structures
{
return new String[0];
}
- // if (modelFileNames == null)
- // {
- // Collection<ChimeraModel> chimodels = viewer.getChimeraModels();
- // _modelFileNameMap = new int[chimodels.size()];
- // int j = 0;
- // for (ChimeraModel chimodel : chimodels)
- // {
- // String mdlName = chimodel.getModelName();
- // }
- // modelFileNames = new String[j];
- // // System.arraycopy(mset, 0, modelFileNames, 0, j);
- // }
return chimeraMaps.keySet().toArray(
modelFileNames = new String[chimeraMaps.size()]);
}
/**
- * map from string to applet
- */
- public Map getRegistryInfo()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- /**
* returns the current sequenceRenderer that should be used to colour the
* structures
*
AlignmentViewPanel alignment);
/**
- * Construct and send a command to highlight zero, one or more atoms.
- *
- * <pre>
- * Done by generating a command like (to 'highlight' position 44)
- * show #0:44.C
- * </pre>
+ * Construct and send a command to highlight zero, one or more atoms. We do
+ * this by sending an "rlabel" command to show the residue label at that
+ * position.
*/
@Override
public void highlightAtoms(List<AtomSpec> atoms)
{
- if (atoms == null)
+ if (atoms == null || atoms.size() == 0)
{
return;
}
- StringBuilder atomSpecs = new StringBuilder();
+
+ StringBuilder cmd = new StringBuilder(128);
boolean first = true;
+ boolean found = false;
for (AtomSpec atom : atoms)
{
List<ChimeraModel> cms = chimeraMaps.get(pdbfile);
if (cms != null && !cms.isEmpty())
{
- atomSpecs.append(first ? "" : ",");
+ if (first)
+ {
+ cmd.append("rlabel #").append(cms.get(0).getModelNumber())
+ .append(":");
+ }
+ else
+ {
+ cmd.append(",");
+ }
first = false;
- atomSpecs.append(cms.get(0).getModelNumber());
- atomSpecs.append(":" + pdbResNum);
+ cmd.append(pdbResNum);
if (!chain.equals(" "))
{
- atomSpecs.append("." + chain);
+ cmd.append(".").append(chain);
}
+ found = true;
}
}
- String atomSpec = atomSpecs.toString();
+ String command = cmd.toString();
/*
- * Avoid repeated commands for the same residue
+ * avoid repeated commands for the same residue
*/
- if (atomSpec.equals(lastMousedOverAtomSpec))
+ if (command.equals(lastHighlightCommand))
{
return;
}
- StringBuilder command = new StringBuilder(32);
- viewerCommandHistory(false);
- if (atomSpec.length() > 0)
+ /*
+ * unshow the label for the previous residue
+ */
+ if (lastHighlightCommand != null)
{
- command.append("show #").append(atomSpec);
- viewer.sendChimeraCommand(command.toString(), false);
+ viewer.sendChimeraCommand("~" + lastHighlightCommand, false);
}
- viewerCommandHistory(true);
- this.lastMousedOverAtomSpec = atomSpec;
+ if (found)
+ {
+ viewer.sendChimeraCommand(command, false);
+ }
+ this.lastHighlightCommand = command;
}
/**
*
* @return
*/
- public List<String> getChainNames()
+
+ /**
+ * Send a 'focus' command to Chimera to recentre the visible display
+ */
+ public void focusView()
{
- List<String> names = new ArrayList<String>();
- String[][] allNames = getChains();
- if (allNames != null)
+ sendChimeraCommand("focus", false);
+ }
+
+ /**
+ * Send a 'show' command for all atoms in the currently selected columns
+ *
+ * TODO: pull up to abstract structure viewer interface
+ *
+ * @param vp
+ */
+ public void highlightSelection(AlignmentViewPanel vp)
+ {
+ List<Integer> cols = vp.getAlignViewport().getColumnSelection()
+ .getSelected();
+ AlignmentI alignment = vp.getAlignment();
+ StructureSelectionManager sm = getSsm();
+ for (SequenceI seq : alignment.getSequences())
{
- for (String[] chainsForPdb : allNames)
+ /*
+ * convert selected columns into sequence positions
+ */
+ int[] positions = new int[cols.size()];
+ int i = 0;
+ for (Integer col : cols)
{
- if (chainsForPdb != null)
- {
- for (String chain : chainsForPdb)
- {
- if (chain != null && !names.contains(chain))
- {
- names.add(chain);
- }
- }
- }
+ positions[i++] = seq.findPosition(col);
}
+ sm.highlightStructure(this, seq, positions);
}
- return names;
}
- /**
- * Send a 'focus' command to Chimera to recentre the visible display
- */
- public void focusView()
+
+ @Override
+ public List<String> getChainNames()
{
- sendChimeraCommand("focus", false);
+ return chainNames;
+ }
+
+ public Hashtable<String, String> getChainFile()
+ {
+ return chainFile;
+ }
+
+ public List<ChimeraModel> getChimeraModelByChain(String chain)
+ {
+ return chimeraMaps.get(chainFile.get(chain));
+ }
+
+ public int getModelNoForChain(String chain)
+ {
+ List<ChimeraModel> foundModels = getChimeraModelByChain(chain);
+ if (foundModels != null && !foundModels.isEmpty())
+ {
+ return foundModels.get(0).getModelNumber();
+ }
+ return -1;
}
}
git://source.jalview.org / jalview.git / blobdiff