/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* @author Jim Procter (jprocter)
*
*/
-public class MouseOverStructureListener extends JSFunctionExec implements
- JsCallBack, StructureListener
+public class MouseOverStructureListener extends JSFunctionExec
+ implements JsCallBack, StructureListener
{
String _listenerfn;
}
@Override
- public String[] getPdbFile()
+ public String[] getStructureFiles()
{
return modelSet;
}
// 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() });
+ new String[]
+ { "mouseover", "" + atom.getPdbFile(), "" + atom.getChain(),
+ "" + (atom.getPdbResNum()), "" + atom.getAtomIndex() });
} catch (Exception ex)
{
System.err.println("Couldn't execute callback with " + _listenerfn
if (JalviewLite.debug)
{
- System.err.println(this.getClass().getName() + " modelSet[0]: "
- + modelSet[0]);
+ System.err.println(
+ this.getClass().getName() + " modelSet[0]: " + modelSet[0]);
ssm.reportMapping();
}
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());
}
;
ArrayList<String[]> ccomands = new ArrayList<String[]>();
ArrayList<String> pdbfn = new ArrayList<String>();
StructureMappingcommandSet[] colcommands = JmolCommands
- .getColourBySequenceCommand(ssm, modelSet, sequence, sr, fr,
- ((AlignmentViewPanel) source).getAlignment());
+ .getColourBySequenceCommand(ssm, modelSet, sequence, sr,
+ (AlignmentViewPanel) source);
if (colcommands == null)
{
return;
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();
}
return _listenerfn;
}
- public void finalise()
- {
- jvlite = null;
- super.finalize();
- }
-
@Override
public void releaseReferences(Object svl)
{