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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
a402ae0
..
47f9df0
100644
(file)
--- a/
src/jalview/appletgui/ExtJmol.java
+++ b/
src/jalview/appletgui/ExtJmol.java
@@
-21,7
+21,6
@@
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.api.SequenceRenderer;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
@@
-35,7
+34,7
@@
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.java.BS;
+import javajs.util.BS;
import org.jmol.viewer.Viewer;
/**
import org.jmol.viewer.Viewer;
/**
@@
-49,12
+48,11
@@
public class ExtJmol extends JalviewJmolBinding
private AlignmentPanel ap;
private AlignmentPanel ap;
- protected ExtJmol(AlignFrame alframe,
- PDBEntry[] pdbentry, SequenceI[][] seq, String[][] chains,
- DataSourceType 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(Viewer viewer, AlignmentPanel alignPanel,
}
public ExtJmol(Viewer viewer, AlignmentPanel alignPanel,
@@
-68,9
+66,6
@@
public class ExtJmol extends JalviewJmolBinding
@Override
public void updateColours(Object source)
{
@Override
public void updateColours(Object source)
{
-
- // TODO Auto-generated method stub
-
}
@Override
}
@Override
@@
-80,20
+75,6
@@
public class ExtJmol extends JalviewJmolBinding
}
@Override
}
@Override
- public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
- {
- AlignmentPanel ap = (AlignmentPanel) alignment;
- if (ap.av.isShowSequenceFeatures())
- {
- 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();
@@
-138,8
+119,8
@@
public class ExtJmol extends JalviewJmolBinding
@Override
public void refreshPdbEntries()
{
@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++)
{
SequenceI[] sq = ap.av.getAlignment().getSequencesArray();
for (int s = 0; s < sq.length; s++)
{
@@
-173,8
+154,8
@@
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);
}
+ show);
}
@@
-182,7
+163,6
@@
public class ExtJmol extends JalviewJmolBinding
protected JmolAppConsoleInterface createJmolConsole(
Container consolePanel, String buttonsToShow)
{
protected JmolAppConsoleInterface createJmolConsole(
Container consolePanel, String buttonsToShow)
{
- // TODO Auto-generated method stub
return null;
}
return null;
}
@@
-195,17
+175,8
@@
public class ExtJmol extends JalviewJmolBinding
}
@Override
}
@Override
- public void releaseReferences(Object svl)
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
public Map<String, Object> getJSpecViewProperty(String arg0)
{
public Map<String, Object> getJSpecViewProperty(String arg0)
{
- // TODO Auto-generated method stub
return null;
}
return null;
}
-
}
}