*/
package jalview.javascript;
-import java.awt.Color;
-import java.util.ArrayList;
-
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.bin.JalviewLite;
import jalview.datamodel.SequenceI;
import jalview.ext.jmol.JmolCommands;
+import jalview.structure.AtomSpec;
import jalview.structure.StructureListener;
import jalview.structure.StructureMapping;
-import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
+import jalview.util.HttpUtils;
+
+import java.util.ArrayList;
+import java.util.List;
/**
* Propagate events involving PDB structures associated with sequences to a
* @author Jim Procter (jprocter)
*
*/
-public class MouseOverStructureListener extends JSFunctionExec implements
- JsCallBack, StructureListener
+public class MouseOverStructureListener extends JSFunctionExec
+ implements JsCallBack, StructureListener
{
String _listenerfn;
{
for (int i = 0; i < modelSet.length; i++)
{
- // resolve a real filename
- try
- {
- if (new java.net.URL(modelSet[i]).openConnection() != null)
- {
- continue;
- }
- } catch (Exception x)
- {
- }
- ;
- try
- {
- String db = jvlite.getDocumentBase().toString();
- db = db.substring(0, db.lastIndexOf("/"));
- if (new java.net.URL(db + "/" + modelSet[i]).openConnection() != null)
- {
- modelSet[i] = db + "/" + modelSet[i];
- continue;
- }
- } catch (Exception x)
- {
- }
- ;
- try
- {
- if (new java.net.URL(jvlite.getCodeBase() + modelSet[i])
- .openConnection() != null)
- {
- modelSet[i] = jvlite.getCodeBase() + modelSet[i];
- continue;
- }
- } catch (Exception x)
- {
- }
- ;
-
+ modelSet[i] = resolveModelFile(modelSet[i]);
}
}
}
+ /**
+ * Returns the first out of: file, file prefixed by document base, or file
+ * prefixed by codebase which can be resolved to a valid URL. If none can,
+ * returns the input parameter value.
+ *
+ * @param file
+ */
+ public String resolveModelFile(String file)
+ {
+ // TODO reuse JalviewLite.LoadingThread.addProtocol instead
+ if (HttpUtils.isValidUrl(file))
+ {
+ return file;
+ }
+
+ String db = jvlite.getDocumentBase().toString();
+ db = db.substring(0, db.lastIndexOf("/"));
+ String docBaseFile = db + "/" + file;
+ if (HttpUtils.isValidUrl(docBaseFile))
+ {
+ return docBaseFile;
+ }
+
+ String cb = jvlite.getCodeBase() + file;
+ if (HttpUtils.isValidUrl(cb))
+ {
+ return cb;
+ }
+
+ return file;
+ }
+
@Override
- public String[] getPdbFile()
+ public String[] getStructureFiles()
{
return modelSet;
}
- @Override
public void mouseOverStructure(int atomIndex, String strInfo)
{
}
@Override
- public void highlightAtom(int atomIndex, int pdbResNum, String chain,
- String pdbId)
+ public void highlightAtoms(List<AtomSpec> atoms)
{
- String[] st = new String[0];
- try
+ for (AtomSpec atom : atoms)
{
- executeJavascriptFunction(_listenerfn, st = new String[]
- { "mouseover", "" + pdbId, "" + chain, "" + (pdbResNum),
- "" + atomIndex });
- } catch (Exception ex)
- {
- System.err.println("Couldn't execute callback with " + _listenerfn
- + " using args { " + st[0] + ", " + st[1] + ", " + st[2]
- + "," + st[3] + "\n");
- ex.printStackTrace();
-
+ try
+ {
+ // TODO is this right? StructureSelectionManager passes pdbFile as the
+ // field that is interpreted (in 2.8.2) as pdbId?
+ // JBPComment: yep - this is right! the Javascript harness uses the
+ // absolute pdbFile URI to locate the PDB file in the external viewer
+ executeJavascriptFunction(_listenerfn,
+ new String[]
+ { "mouseover", "" + atom.getPdbFile(), "" + atom.getChain(),
+ "" + (atom.getPdbResNum()), "" + atom.getAtomIndex() });
+ } catch (Exception ex)
+ {
+ System.err.println("Couldn't execute callback with " + _listenerfn
+ + " for atomSpec: " + atom);
+ ex.printStackTrace();
+ }
}
-
}
@Override
final Object source = srce;
StructureSelectionManager ssm = StructureSelectionManager
.getStructureSelectionManager(jvlite);
- // if (jvlite.debug)
- // {
- // ssm.reportMapping();
- // }
+
+ if (JalviewLite.debug)
+ {
+ System.err.println(
+ this.getClass().getName() + " modelSet[0]: " + modelSet[0]);
+ ssm.reportMapping();
+ }
+
if (source instanceof jalview.api.AlignmentViewPanel)
{
SequenceI[][] sequence = new SequenceI[modelSet.length][];
SequenceRenderer sr = ((jalview.appletgui.AlignmentPanel) source)
.getSequenceRenderer();
FeatureRenderer fr = ((jalview.appletgui.AlignmentPanel) source).av
- .isShowSequenceFeatures() ? new jalview.appletgui.FeatureRenderer(
- ((jalview.appletgui.AlignmentPanel) source).av) : null;
+ .isShowSequenceFeatures()
+ ? new jalview.appletgui.FeatureRenderer(
+ ((jalview.appletgui.AlignmentPanel) source).av)
+ : null;
if (fr != null)
{
- ((jalview.appletgui.FeatureRenderer) fr)
- .transferSettings(((jalview.appletgui.AlignmentPanel) source)
+ ((jalview.appletgui.FeatureRenderer) fr).transferSettings(
+ ((jalview.appletgui.AlignmentPanel) source)
.getFeatureRenderer());
}
;
// Form a colour command from the given alignment panel for each distinct
// structure
- ArrayList<String[]> ccomands = new ArrayList<String[]>();
- ArrayList<String> pdbfn = new ArrayList<String>();
- StructureMappingcommandSet[] colcommands = JmolCommands
- .getColourBySequenceCommand(ssm, modelSet, sequence, sr, fr,
- ((AlignmentViewPanel) source).getAlignment());
+ ArrayList<String[]> ccomands = new ArrayList<>();
+ ArrayList<String> pdbfn = new ArrayList<>();
+ String[] colcommands = new JmolCommands().colourBySequence(ssm,
+ modelSet, sequence, sr, (AlignmentViewPanel) source);
if (colcommands == null)
{
return;
}
int sz = 0;
- for (jalview.structure.StructureMappingcommandSet ccset : colcommands)
+ // for (jalview.structure.StructureMappingcommandSet ccset : colcommands)
+ for (String command : colcommands)
{
- sz += ccset.commands.length;
- ccomands.add(ccset.commands);
- pdbfn.add(ccset.mapping);
+ // sz += ccset.commands.length;
+ // ccomands.add(command); // ccset.commands);
+ // pdbfn.add(ccset.mapping);
}
String mclass, mhandle;
System.arraycopy(ccset, 0, ccomandset, sz, ccset.length);
sz += ccset.length;
}
- if (jvlite.isJsMessageSetChanged(
- mclass = "colourstruct",
+ if (jvlite.isJsMessageSetChanged(mclass = "colourstruct",
mhandle = ((jalview.appletgui.AlignmentPanel) source).av
- .getViewId(), ccomandset))
+ .getViewId(),
+ ccomandset))
{
jvlite.setJsMessageSet(mclass, mhandle, ccomandset);
// and notify javascript handler
- String st[] = new String[]
- {
- "colourstruct",
+ String st[] = new String[] { "colourstruct",
"" + ((jalview.appletgui.AlignmentPanel) source).av.getViewId(),
- "" + ccomandset.length,
- jvlite.arrayToSeparatorList(pdbfn.toArray(new String[pdbfn
- .size()])) };
+ "" + ccomandset.length, jvlite.arrayToSeparatorList(
+ pdbfn.toArray(new String[pdbfn.size()])) };
try
{
executeJavascriptFunction(true, _listenerfn, st);
} catch (Exception ex)
{
- System.err.println("Couldn't execute callback with "
- + _listenerfn + " using args { " + st[0] + ", " + st[1]
- + ", " + st[2] + "," + st[3] + "}"); // + ","+st[4]+"\n");
+ System.err.println("Couldn't execute callback with " + _listenerfn
+ + " using args { " + st[0] + ", " + st[1] + ", " + st[2]
+ + "," + st[3] + "}"); // + ","+st[4]+"\n");
ex.printStackTrace();
}
}
@Override
- public Color getColour(int atomIndex, int pdbResNum, String chain,
- String pdbId)
- {
- return null;
- }
-
- @Override
public AlignFrame getAlignFrame()
{
// associated with all alignframes, always.
return _listenerfn;
}
- public void finalise()
- {
- jvlite = null;
- super.finalize();
- }
-
@Override
public void releaseReferences(Object svl)
{
}
+ @Override
+ public boolean isListeningFor(SequenceI seq)
+ {
+ return true;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff