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JAL-2465 bugfix and rerefactor renamed getPdbFile() method to getStructureFile()
[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
5866d51
..
d37975d
100644
(file)
--- a/
src/jalview/ext/jmol/JmolParser.java
+++ b/
src/jalview/ext/jmol/JmolParser.java
@@
-24,6
+24,7
@@
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.datamodel.Annotation;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
import jalview.io.FileParse;
import jalview.io.StructureFile;
import jalview.schemes.ResidueProperties;
import jalview.io.FileParse;
import jalview.io.StructureFile;
import jalview.schemes.ResidueProperties;
@@
-38,8
+39,6
@@
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;
@@
-61,9
+60,10
@@
public class JmolParser extends StructureFile implements JmolStatusListener
{
Viewer viewer = null;
{
Viewer viewer = null;
- public JmolParser(String inFile, String type) throws IOException
+ public JmolParser(String inFile, DataSourceType sourceType)
+ throws IOException
{
{
- super(inFile, type);
+ super(inFile, sourceType);
}
public JmolParser(FileParse fp) throws IOException
}
public JmolParser(FileParse fp) throws IOException
@@
-154,10
+154,12
@@
public class JmolParser extends StructureFile implements JmolStatusListener
if (pdbId == null)
{
setId(safeName(getDataName()));
if (pdbId == null)
{
setId(safeName(getDataName()));
+ setPDBIdAvailable(false);
}
else
{
setId(pdbId);
}
else
{
setId(pdbId);
+ setPDBIdAvailable(true);
}
List<Atom> significantAtoms = convertSignificantAtoms(ms);
for (Atom tmpatom : significantAtoms)
}
List<Atom> significantAtoms = convertSignificantAtoms(ms);
for (Atom tmpatom : significantAtoms)
@@
-184,6
+186,14
@@
public class JmolParser extends StructureFile implements JmolStatusListener
makeResidueList();
makeCaBondList();
makeResidueList();
makeCaBondList();
+ if (getId() == null)
+ {
+ // always use resource name, not the hardwired file
+ // Does the value of ID get used ? Behaviour needs to be
+ // documented and tested
+ setId(getDataName());
+ }
+
for (PDBChain chain : getChains())
{
SequenceI chainseq = postProcessChain(chain);
for (PDBChain chain : getChains())
{
SequenceI chainseq = postProcessChain(chain);
@@
-470,7
+480,7
@@
public class JmolParser extends StructureFile implements JmolStatusListener
* Not implemented - returns null
*/
@Override
* Not implemented - returns null
*/
@Override
- public String print()
+ public String print(SequenceI[] seqs, boolean jvSuffix)
{
return null;
}
{
return null;
}
@@
-624,7
+634,7
@@
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;
}