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JAL-2177 Jmol update from: Jmol-14.2.14_2015.06.11 to Jmol-14.6.4_2016.10.26
[jalview.git]
/
src
/
jalview
/
ext
/
jmol
/
JmolParser.java
diff --git
a/src/jalview/ext/jmol/JmolParser.java
b/src/jalview/ext/jmol/JmolParser.java
index
ca45d7b
..
180da8f
100644
(file)
--- a/
src/jalview/ext/jmol/JmolParser.java
+++ b/
src/jalview/ext/jmol/JmolParser.java
@@
-38,8
+38,6
@@
import java.util.List;
import java.util.Map;
import java.util.Vector;
import java.util.Map;
import java.util.Vector;
-import javajs.awt.Dimension;
-
import org.jmol.api.JmolStatusListener;
import org.jmol.api.JmolViewer;
import org.jmol.c.CBK;
import org.jmol.api.JmolStatusListener;
import org.jmol.api.JmolViewer;
import org.jmol.c.CBK;
@@
-150,7
+148,17
@@
public class JmolParser extends StructureFile implements JmolStatusListener
List<SequenceI> prot = new ArrayList<SequenceI>();
PDBChain tmpchain;
String pdbId = (String) ms.getInfo(0, "title");
List<SequenceI> prot = new ArrayList<SequenceI>();
PDBChain tmpchain;
String pdbId = (String) ms.getInfo(0, "title");
- setId(pdbId);
+
+ if (pdbId == null)
+ {
+ setId(safeName(getDataName()));
+ setPDBIdAvailable(false);
+ }
+ else
+ {
+ setId(pdbId);
+ setPDBIdAvailable(true);
+ }
List<Atom> significantAtoms = convertSignificantAtoms(ms);
for (Atom tmpatom : significantAtoms)
{
List<Atom> significantAtoms = convertSignificantAtoms(ms);
for (Atom tmpatom : significantAtoms)
{
@@
-165,7
+173,7
@@
public class JmolParser extends StructureFile implements JmolStatusListener
tmpchain.atoms.addElement(tmpatom);
} catch (Exception e)
{
tmpchain.atoms.addElement(tmpatom);
} catch (Exception e)
{
- tmpchain = new PDBChain(pdbId, tmpatom.chain);
+ tmpchain = new PDBChain(getId(), tmpatom.chain);
getChains().add(tmpchain);
tmpchain.atoms.addElement(tmpatom);
}
getChains().add(tmpchain);
tmpchain.atoms.addElement(tmpatom);
}
@@
-176,10
+184,6
@@
public class JmolParser extends StructureFile implements JmolStatusListener
makeResidueList();
makeCaBondList();
makeResidueList();
makeCaBondList();
- if (getId() == null)
- {
- setId(safeName(getDataName()));
- }
for (PDBChain chain : getChains())
{
SequenceI chainseq = postProcessChain(chain);
for (PDBChain chain : getChains())
{
SequenceI chainseq = postProcessChain(chain);
@@
-620,7
+624,7
@@
public class JmolParser extends StructureFile implements JmolStatusListener
* Not implemented - returns null
*/
@Override
* Not implemented - returns null
*/
@Override
- public Dimension resizeInnerPanel(String data)
+ public int[] resizeInnerPanel(String data)
{
return null;
}
{
return null;
}