/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * 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.
*
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.ext.jmol.JalviewJmolBinding;
+import jalview.io.DataSourceType;
import java.awt.Container;
import java.util.ArrayList;
private AlignmentPanel ap;
- protected ExtJmol(jalview.appletgui.AlignFrame alframe,
- PDBEntry[] pdbentry, SequenceI[][] seq, String[][] chains,
- String protocol)
+ protected ExtJmol(AlignFrame alframe, PDBEntry[] pdbentry,
+ SequenceI[][] seq, DataSourceType protocol)
{
super(alframe.alignPanel.getStructureSelectionManager(), pdbentry, seq,
- chains, protocol);
+ protocol);
}
public ExtJmol(Viewer viewer, AlignmentPanel alignPanel,
notifyFileLoaded(null, null, null, null, 0);
}
+ @Override
public void updateColours(Object source)
{
-
- // TODO Auto-generated method stub
-
}
+ @Override
public void showUrl(String arg0)
{
showUrl(arg0, "jmol");
@Override
public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
{
- AlignmentPanel ap = (AlignmentPanel) alignment;
- if (ap.av.isShowSequenceFeatures())
+ AlignmentPanel alignPanel = (AlignmentPanel) alignment;
+ if (alignPanel.av.isShowSequenceFeatures())
{
- return ap.getFeatureRenderer();
+ return alignPanel.getFeatureRenderer();
}
else
{
}
}
+
@Override
public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
{
// ignore
}
+ @Override
public void selectionChanged(BS arg0)
{
System.out.println(arg0);
@Override
public void refreshPdbEntries()
{
- List<PDBEntry> pdbe = new ArrayList<PDBEntry>();
- List<String> fileids = new ArrayList<String>();
+ List<PDBEntry> pdbe = new ArrayList<>();
+ List<String> fileids = new ArrayList<>();
SequenceI[] sq = ap.av.getAlignment().getSequencesArray();
for (int s = 0; s < sq.length; s++)
{
{
// This never gets called because we haven't overriden the associated Jmol's
// console
- System.err
- .println("WARNING: unexpected call to ExtJmol's showConsole method. (showConsole="
+ System.err.println(
+ "WARNING: unexpected call to ExtJmol's showConsole method. (showConsole="
+ show);
}
protected JmolAppConsoleInterface createJmolConsole(
Container consolePanel, String buttonsToShow)
{
- // TODO Auto-generated method stub
return null;
}
@Override
public void releaseReferences(Object svl)
{
- // TODO Auto-generated method stub
-
}
@Override
public Map<String, Object> getJSpecViewProperty(String arg0)
{
- // TODO Auto-generated method stub
return null;
}