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Merge branch 'develop' into feature/JAL-3390hideUnmappedStructure
[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
2a510a2
..
a9c5f5c
100644
(file)
--- a/
src/jalview/ext/jmol/JmolParser.java
+++ b/
src/jalview/ext/jmol/JmolParser.java
@@
-45,9
+45,9
@@
import org.jmol.c.STR;
import org.jmol.modelset.ModelSet;
import org.jmol.viewer.Viewer;
import org.jmol.modelset.ModelSet;
import org.jmol.viewer.Viewer;
-import MCview.Atom;
-import MCview.PDBChain;
-import MCview.Residue;
+import mc_view.Atom;
+import mc_view.PDBChain;
+import mc_view.Residue;
/**
* Import and process files with Jmol for file like PDB, mmCIF
/**
* Import and process files with Jmol for file like PDB, mmCIF
@@
-59,13
+59,14
@@
public class JmolParser extends StructureFile implements JmolStatusListener
{
Viewer viewer = null;
{
Viewer viewer = null;
- public JmolParser(boolean immediate, String inFile,
+ public JmolParser(boolean immediate, Object inFile,
DataSourceType sourceType) throws IOException
{
DataSourceType sourceType) throws IOException
{
+ // BH 2018 File or String for filename
super(immediate, inFile, sourceType);
}
super(immediate, inFile, sourceType);
}
- public JmolParser(String inFile, DataSourceType sourceType)
+ public JmolParser(Object inFile, DataSourceType sourceType)
throws IOException
{
super(inFile, sourceType);
throws IOException
{
super(inFile, sourceType);
@@
-133,8
+134,8
@@
public class JmolParser extends StructureFile implements JmolStatusListener
* params -o (output to sysout) -n (nodisplay) -x (exit when finished)
* see http://wiki.jmol.org/index.php/Jmol_Application
*/
* params -o (output to sysout) -n (nodisplay) -x (exit when finished)
* see http://wiki.jmol.org/index.php/Jmol_Application
*/
- viewer = (Viewer) JmolViewer.allocateViewer(null, null, null, null,
- null, "-x -o -n", this);
+
+ viewer = JalviewJmolBinding.getJmolData(this);
// ensure the 'new' (DSSP) not 'old' (Ramachandran) SS method is used
viewer.setBooleanProperty("defaultStructureDSSP", true);
} catch (ClassCastException x)
// ensure the 'new' (DSSP) not 'old' (Ramachandran) SS method is used
viewer.setBooleanProperty("defaultStructureDSSP", true);
} catch (ClassCastException x)
@@
-171,16
+172,16
@@
public class JmolParser extends StructureFile implements JmolStatusListener
List<Atom> significantAtoms = convertSignificantAtoms(ms);
for (Atom tmpatom : significantAtoms)
{
List<Atom> significantAtoms = convertSignificantAtoms(ms);
for (Atom tmpatom : significantAtoms)
{
- try
+ if (tmpatom.resNumIns.trim().equals(lastID))
+ {
+ // phosphorylated protein - seen both CA and P..
+ continue;
+ }
+ tmpchain = findChain(tmpatom.chain);
+ if (tmpchain != null)
{
{
- tmpchain = findChain(tmpatom.chain);
- if (tmpatom.resNumIns.trim().equals(lastID))
- {
- // phosphorylated protein - seen both CA and P..
- continue;
- }
tmpchain.atoms.addElement(tmpatom);
tmpchain.atoms.addElement(tmpatom);
- } catch (Exception e)
+ } else
{
tmpchain = new PDBChain(getId(), tmpatom.chain);
getChains().add(tmpchain);
{
tmpchain = new PDBChain(getId(), tmpatom.chain);
getChains().add(tmpchain);