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JAL-2791 refactored Export Features to apply all visibility tests
[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
dc3d0ee
..
2a510a2
100644
(file)
--- a/
src/jalview/ext/jmol/JmolParser.java
+++ b/
src/jalview/ext/jmol/JmolParser.java
@@
-28,7
+28,6
@@
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;
-import jalview.structure.StructureImportSettings;
import jalview.util.Format;
import jalview.util.MessageManager;
import jalview.util.Format;
import jalview.util.MessageManager;
@@
-60,6
+59,12
@@
public class JmolParser extends StructureFile implements JmolStatusListener
{
Viewer viewer = null;
{
Viewer viewer = null;
+ public JmolParser(boolean immediate, String inFile,
+ DataSourceType sourceType) throws IOException
+ {
+ super(immediate, inFile, sourceType);
+ }
+
public JmolParser(String inFile, DataSourceType sourceType)
throws IOException
{
public JmolParser(String inFile, DataSourceType sourceType)
throws IOException
{
@@
-183,7
+188,11
@@
public class JmolParser extends StructureFile implements JmolStatusListener
}
lastID = tmpatom.resNumIns.trim();
}
}
lastID = tmpatom.resNumIns.trim();
}
- xferSettings();
+ if (isParseImmediately())
+ {
+ // configure parsing settings from the static singleton
+ xferSettings();
+ }
makeResidueList();
makeCaBondList();
makeResidueList();
makeCaBondList();
@@
-200,7
+209,8
@@
public class JmolParser extends StructureFile implements JmolStatusListener
prot.add(chainseq);
}
prot.add(chainseq);
}
- if (StructureImportSettings.isProcessSecondaryStructure())
+ // look at local setting for adding secondary tructure
+ if (predictSecondaryStructure)
{
createAnnotation(chainseq, chain, ms.at);
}
{
createAnnotation(chainseq, chain, ms.at);
}