import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.httpserver.AbstractRequestHandler;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ResidueProperties;
import jalview.structure.AtomSpec;
+import jalview.structure.StructureMapping;
import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.Comparison;
import jalview.util.MessageManager;
import java.awt.Color;
private String lastCommand;
- private boolean loadedInline;
-
- /**
- * current set of model filenames loaded
- */
- String[] modelFileNames = null;
-
String lastHighlightCommand;
- private List<String> lastReply;
-
/*
* incremented every time a load notification is successfully handled -
* lightweight mechanism for other threads to detect when they can start
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
}
/**
- * 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' positions 44 and 46)
- * show #0:44,46.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 cmd = new StringBuilder(128);
boolean first = true;
boolean found = false;
{
if (first)
{
- cmd.append("show #").append(cms.get(0).getModelNumber())
+ cmd.append("rlabel #").append(cms.get(0).getModelNumber())
.append(":");
}
else
cmd.append(",");
}
first = false;
- cmd.append(cms.get(0).getModelNumber()).append(":");
cmd.append(pdbResNum);
if (!chain.equals(" "))
{
String command = cmd.toString();
/*
- * Avoid repeated commands for the same residue
+ * avoid repeated commands for the same residue
*/
if (command.equals(lastHighlightCommand))
{
return;
}
- viewerCommandHistory(false);
+ /*
+ * unshow the label for the previous residue
+ */
+ if (lastHighlightCommand != null)
+ {
+ viewer.sendChimeraCommand("~" + lastHighlightCommand, false);
+ }
if (found)
{
- viewer.sendChimeraCommand(command.toString(), false);
+ viewer.sendChimeraCommand(command, false);
}
- viewerCommandHistory(true);
this.lastHighlightCommand = command;
}
sm.highlightStructure(this, seq, positions);
}
}
+
+ /**
+ * Constructs and send commands to Chimera to set attributes on residues for
+ * features visible in Jalview
+ *
+ * @param avp
+ */
+ public void sendFeaturesToChimera(AlignmentViewPanel avp)
+ {
+ // TODO send a command per feature with the range of residues it applies to
+ AlignmentI alignment = avp.getAlignment();
+ FeatureRenderer fr = getFeatureRenderer(avp);
+
+ /*
+ * fr is null if feature display is turned off
+ */
+ if (fr == null)
+ {
+ return;
+ }
+
+ String[] files = getPdbFile();
+ if (files == null)
+ {
+ return;
+ }
+ for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+ {
+ StructureMapping[] mapping = getSsm().getMapping(files[pdbfnum]);
+
+ if (mapping == null || mapping.length < 1)
+ {
+ continue;
+ }
+
+ int lastPos = -1;
+ for (int seqNo = 0; seqNo < getSequence()[pdbfnum].length; seqNo++)
+ {
+ for (int m = 0; m < mapping.length; m++)
+ {
+ final SequenceI seq = getSequence()[pdbfnum][seqNo];
+ int sp = alignment.findIndex(seq);
+ if (mapping[m].getSequence() == seq && sp > -1)
+ {
+ SequenceI asp = alignment.getSequenceAt(sp);
+ for (int r = 0; r < asp.getLength(); r++)
+ {
+ // no mapping to gaps in sequence
+ if (Comparison.isGap(asp.getCharAt(r)))
+ {
+ continue;
+ }
+ int residuePos = asp.findPosition(r);
+ int pos = mapping[m].getPDBResNum(residuePos);
+
+ if (pos < 1 || pos == lastPos)
+ {
+ continue;
+ }
+ final String chain = mapping[m].getChain();
+ List<SequenceFeature> features = fr.findFeaturesAtRes(asp,
+ residuePos);
+ for (SequenceFeature feature : features)
+ {
+ String desc = feature.getDescription();
+ float score = feature.getScore();
+ if (score != 0 && score != Float.NaN)
+ {
+ desc = Float.toString(score);
+ }
+ String attName = "jv:"
+ + feature.getType().replace(" ", "_");
+ String cmd = "setattr r " + attName + " \""
+ + desc + "\" #" + pdbfnum + ":" + pos + "." + chain;
+ System.out.println(cmd);
+ sendAsynchronousCommand(cmd, null);
+ }
+ }
+ }
+ }
+ }
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff