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JAL-629 example files from nf-core
[jalview.git]
/
src
/
jalview
/
appletgui
/
ExtJmol.java
diff --git
a/src/jalview/appletgui/ExtJmol.java
b/src/jalview/appletgui/ExtJmol.java
index
58bd5a6
..
47f9df0
100644
(file)
--- a/
src/jalview/appletgui/ExtJmol.java
+++ b/
src/jalview/appletgui/ExtJmol.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 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.
*
*
* This file is part of Jalview.
*
@@
-21,20
+21,21
@@
package jalview.appletgui;
import jalview.api.AlignmentViewPanel;
package jalview.appletgui;
import jalview.api.AlignmentViewPanel;
-import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.ext.jmol.JalviewJmolBinding;
import jalview.api.SequenceRenderer;
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;
import java.awt.Container;
import java.util.ArrayList;
-import java.util.BitSet;
import java.util.List;
import java.util.List;
+import java.util.Map;
import java.util.Vector;
import org.jmol.api.JmolAppConsoleInterface;
import java.util.Vector;
import org.jmol.api.JmolAppConsoleInterface;
-import org.jmol.api.JmolViewer;
+import javajs.util.BS;
+import org.jmol.viewer.Viewer;
/**
* bind an alignment view to an external Jmol instance.
/**
* bind an alignment view to an external Jmol instance.
@@
-47,15
+48,14
@@
public class ExtJmol extends JalviewJmolBinding
private AlignmentPanel ap;
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,
{
super(alframe.alignPanel.getStructureSelectionManager(), pdbentry, seq,
- chains, protocol);
+ protocol);
}
}
- public ExtJmol(JmolViewer viewer, AlignmentPanel alignPanel,
+ public ExtJmol(Viewer viewer, AlignmentPanel alignPanel,
SequenceI[][] seqs)
{
super(alignPanel.getStructureSelectionManager(), seqs, viewer);
SequenceI[][] seqs)
{
super(alignPanel.getStructureSelectionManager(), seqs, viewer);
@@
-63,79
+63,73
@@
public class ExtJmol extends JalviewJmolBinding
notifyFileLoaded(null, null, null, null, 0);
}
notifyFileLoaded(null, null, null, null, 0);
}
+ @Override
public void updateColours(Object source)
{
public void updateColours(Object source)
{
-
- // TODO Auto-generated method stub
-
}
}
+ @Override
public void showUrl(String arg0)
{
showUrl(arg0, "jmol");
}
public void showUrl(String arg0)
{
showUrl(arg0, "jmol");
}
- public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
- {
- AlignmentPanel ap = (AlignmentPanel) alignment;
- if (ap.av.showSequenceFeatures)
- {
- return ap.getFeatureRenderer();
- }
- else
- {
- return null;
- }
- }
-
+ @Override
public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
{
return ((AlignmentPanel) alignment).getSequenceRenderer();
}
public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
{
return ((AlignmentPanel) alignment).getSequenceRenderer();
}
+ @Override
public void notifyScriptTermination(String strStatus, int msWalltime)
{
// ignore
}
public void notifyScriptTermination(String strStatus, int msWalltime)
{
// ignore
}
+ @Override
public void sendConsoleEcho(String strEcho)
{
// ignore
}
public void sendConsoleEcho(String strEcho)
{
// ignore
}
+ @Override
public void sendConsoleMessage(String strStatus)
{
// ignore
}
public void sendConsoleMessage(String strStatus)
{
// ignore
}
+ @Override
public void showUrl(String url, String target)
{
ap.alignFrame.showURL(url, target);
}
public void showUrl(String url, String target)
{
ap.alignFrame.showURL(url, target);
}
+ @Override
public void refreshGUI()
{
// ignore
}
public void refreshGUI()
{
// ignore
}
- public void selectionChanged(BitSet arg0)
+ @Override
+ public void selectionChanged(BS arg0)
{
System.out.println(arg0);
}
{
System.out.println(arg0);
}
+ @Override
public void refreshPdbEntries()
{
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++)
{
SequenceI[] sq = ap.av.getAlignment().getSequencesArray();
for (int s = 0; s < sq.length; s++)
{
- Vector pdbids = sq[s].getPDBId();
+ Vector<PDBEntry> pdbids = sq[s].getAllPDBEntries();
if (pdbids != null)
{
for (int pe = 0, peSize = pdbids.size(); pe < peSize; pe++)
{
if (pdbids != null)
{
for (int pe = 0, peSize = pdbids.size(); pe < peSize; pe++)
{
- PDBEntry pentry = (PDBEntry) pdbids.elementAt(pe);
+ PDBEntry pentry = pdbids.elementAt(pe);
if (!fileids.contains(pentry.getId()))
{
pdbe.add(pentry);
if (!fileids.contains(pentry.getId()))
{
pdbe.add(pentry);
@@
-160,16
+154,15
@@
public class ExtJmol extends JalviewJmolBinding
{
// This never gets called because we haven't overriden the associated Jmol's
// console
{
// 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);
}
@Override
+ show);
}
@Override
- protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2,
+ protected JmolAppConsoleInterface createJmolConsole(
Container consolePanel, String buttonsToShow)
{
Container consolePanel, String buttonsToShow)
{
- // TODO Auto-generated method stub
return null;
}
return null;
}
@@
-182,10
+175,8
@@
public class ExtJmol extends JalviewJmolBinding
}
@Override
}
@Override
- public void releaseReferences(Object svl)
+ public Map<String, Object> getJSpecViewProperty(String arg0)
{
{
- // TODO Auto-generated method stub
-
+ return null;
}
}
-
}
}