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Merge branch 'bug/JAL-3244jmolWindows' into develop
[jalview.git]
/
src
/
jalview
/
appletgui
/
ExtJmol.java
diff --git
a/src/jalview/appletgui/ExtJmol.java
b/src/jalview/appletgui/ExtJmol.java
index
5ffbaa4
..
b0d3f7a
100644
(file)
--- a/
src/jalview/appletgui/ExtJmol.java
+++ b/
src/jalview/appletgui/ExtJmol.java
@@
-26,6
+26,7
@@
import jalview.api.SequenceRenderer;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.ext.jmol.JalviewJmolBinding;
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;
@@
-48,9
+49,8
@@
public class ExtJmol extends JalviewJmolBinding
private AlignmentPanel ap;
private AlignmentPanel ap;
- protected ExtJmol(jalview.appletgui.AlignFrame alframe,
- PDBEntry[] pdbentry, SequenceI[][] seq,
- String protocol)
+ protected ExtJmol(AlignFrame alframe, PDBEntry[] pdbentry,
+ SequenceI[][] seq, DataSourceType protocol)
{
super(alframe.alignPanel.getStructureSelectionManager(), pdbentry, seq,
protocol);
{
super(alframe.alignPanel.getStructureSelectionManager(), pdbentry, seq,
protocol);
@@
-67,9
+67,6
@@
public class ExtJmol extends JalviewJmolBinding
@Override
public void updateColours(Object source)
{
@Override
public void updateColours(Object source)
{
-
- // TODO Auto-generated method stub
-
}
@Override
}
@Override
@@
-81,10
+78,10
@@
public class ExtJmol extends JalviewJmolBinding
@Override
public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
{
@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
{
}
else
{
@@
-92,6
+89,7
@@
public class ExtJmol extends JalviewJmolBinding
}
}
}
}
+
@Override
public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
{
@Override
public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
{
@@
-137,8
+135,8
@@
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++)
{
@@
-172,8
+170,8
@@
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);
}
@@
-181,7
+179,6
@@
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;
}
@@
-196,14
+193,11
@@
public class ExtJmol extends JalviewJmolBinding
@Override
public void releaseReferences(Object svl)
{
@Override
public void releaseReferences(Object svl)
{
- // TODO Auto-generated method stub
-
}
@Override
public Map<String, Object> getJSpecViewProperty(String arg0)
{
}
@Override
public Map<String, Object> getJSpecViewProperty(String arg0)
{
- // TODO Auto-generated method stub
return null;
}
return null;
}