/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
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.appletgui.AlignFrame;
+import jalview.appletgui.AlignmentPanel;
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 java.util.ArrayList;
+import java.util.List;
+
/**
* Propagate events involving PDB structures associated with sequences to a
* javascript function. Generally, the javascript handler is called with a
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
// {
// ssm.reportMapping();
// }
- if (source instanceof jalview.api.AlignmentViewPanel)
+ if (source instanceof AlignmentViewPanel)
{
SequenceI[][] sequence = new SequenceI[modelSet.length][];
for (int m = 0; m < modelSet.length; m++)
// }
}
- SequenceRenderer sr = ((jalview.appletgui.AlignmentPanel) source)
+ SequenceRenderer sr = ((AlignmentPanel) source)
.getSequenceRenderer();
- FeatureRenderer fr = ((jalview.appletgui.AlignmentPanel) source).av
- .getShowSequenceFeatures() ? new jalview.appletgui.FeatureRenderer(
- ((jalview.appletgui.AlignmentPanel) source).av) : null;
+ FeatureRenderer fr = ((AlignmentPanel) source).av
+ .isShowSequenceFeatures() ? new jalview.appletgui.FeatureRenderer(
+ ((AlignmentPanel) source).av) : null;
if (fr != null)
{
((jalview.appletgui.FeatureRenderer) fr)
- .transferSettings(((jalview.appletgui.AlignmentPanel) source)
+ .transferSettings(((AlignmentPanel) source)
.getFeatureRenderer());
}
;
return;
}
int sz = 0;
- for (jalview.structure.StructureMappingcommandSet ccset : colcommands)
+ for (StructureMappingcommandSet ccset : colcommands)
{
sz += ccset.commands.length;
ccomands.add(ccset.commands);
}
if (jvlite.isJsMessageSetChanged(
mclass = "colourstruct",
- mhandle = ((jalview.appletgui.AlignmentPanel) source).av
+ mhandle = ((AlignmentPanel) source).av
.getViewId(), ccomandset))
{
jvlite.setJsMessageSet(mclass, mhandle, ccomandset);
String st[] = new String[]
{
"colourstruct",
- "" + ((jalview.appletgui.AlignmentPanel) source).av.getViewId(),
+ "" + ((AlignmentPanel) source).av.getViewId(),
"" + ccomandset.length,
jvlite.arrayToSeparatorList(pdbfn.toArray(new String[pdbfn
.size()])) };
}
@Override
- public Color getColour(int atomIndex, int pdbResNum, String chain,
- String pdbId)
- {
- return null;
- }
-
- @Override
public AlignFrame getAlignFrame()
{
// associated with all alignframes, always.
}
+ @Override
+ public boolean isListeningFor(SequenceI seq)
+ {
+ return true;
+ }
+
}