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Merge branch 'develop' into bug/JAL-2210_ensembl_uniprot_primaryrefs_alternate
[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
2cb7559
..
65b4b96
100644
(file)
--- a/
src/jalview/ext/jmol/JmolParser.java
+++ b/
src/jalview/ext/jmol/JmolParser.java
@@
-28,6
+28,7
@@
import jalview.io.FileParse;
import jalview.io.StructureFile;
import jalview.schemes.ResidueProperties;
import jalview.structure.StructureImportSettings;
import jalview.io.StructureFile;
import jalview.schemes.ResidueProperties;
import jalview.structure.StructureImportSettings;
+import jalview.util.Format;
import jalview.util.MessageManager;
import java.io.IOException;
import jalview.util.MessageManager;
import java.io.IOException;
@@
-60,15
+61,13
@@
public class JmolParser extends StructureFile implements JmolStatusListener
{
Viewer viewer = null;
{
Viewer viewer = null;
- public JmolParser(boolean addAlignmentAnnotations, boolean predictSecStr,
- boolean externalSecStr, String inFile, String type)
+ public JmolParser(String inFile, String type)
throws IOException
{
super(inFile, type);
}
throws IOException
{
super(inFile, type);
}
- public JmolParser(boolean addAlignmentAnnotations, boolean predictSecStr,
- boolean externalSecStr, FileParse fp) throws IOException
+ public JmolParser(FileParse fp) throws IOException
{
super(fp);
}
{
super(fp);
}
@@
-125,8
+124,13
@@
public class JmolParser extends StructureFile implements JmolStatusListener
{
try
{
{
try
{
+ /*
+ * params -o (output to sysout) -i (no info logging, less verbose)
+ * -n (nodisplay) -x (exit when finished)
+ * see http://wiki.jmol.org/index.php/Jmol_Application
+ */
viewer = (Viewer) JmolViewer.allocateViewer(null, null, null, null,
viewer = (Viewer) JmolViewer.allocateViewer(null, null, null, null,
- null, "-x -o -n", this);
+ null, "-x -o -n -i", 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)
@@
-230,8
+234,8
@@
public class JmolParser extends StructureFile implements JmolStatusListener
curAtom.resNumber = atom.getResno();
curAtom.occupancy = ms.occupancies != null ? ms.occupancies[atom
.getIndex()] : Float.valueOf(atom.getOccupancy100());
curAtom.resNumber = atom.getResno();
curAtom.occupancy = ms.occupancies != null ? ms.occupancies[atom
.getIndex()] : Float.valueOf(atom.getOccupancy100());
- curAtom.resNumIns = ("" + curAtom.resNumber + curAtom.insCode)
- .trim();
+ String fmt = new Format("%4i").form(curAtom.resNumber);
+ curAtom.resNumIns = (fmt + curAtom.insCode);
curAtom.tfactor = atom.getBfactor100() / 100f;
curAtom.type = 0;
// significantAtoms.add(curAtom);
curAtom.tfactor = atom.getBfactor100() / 100f;
curAtom.type = 0;
// significantAtoms.add(curAtom);
@@
-270,6
+274,10
@@
public class JmolParser extends StructureFile implements JmolStatusListener
// diff < 5 then mark as valid and update termination Atom
if (chainTerMap.containsKey(curAtomChId))
{
// diff < 5 then mark as valid and update termination Atom
if (chainTerMap.containsKey(curAtomChId))
{
+ if (curAtom.getResno() < chainTerMap.get(curAtomChId).getResno())
+ {
+ return false;
+ }
if ((curAtom.getResno() - chainTerMap.get(curAtomChId).getResno()) < 5)
{
chainTerMap.put(curAtomChId, curAtom);
if ((curAtom.getResno() - chainTerMap.get(curAtomChId).getResno()) < 5)
{
chainTerMap.put(curAtomChId, curAtom);
@@
-281,6
+289,10
@@
public class JmolParser extends StructureFile implements JmolStatusListener
// atom with previously terminated chain encountered
else if (chainTerMap.containsKey(curAtomChId))
{
// atom with previously terminated chain encountered
else if (chainTerMap.containsKey(curAtomChId))
{
+ if (curAtom.getResno() < chainTerMap.get(curAtomChId).getResno())
+ {
+ return false;
+ }
if ((curAtom.getResno() - chainTerMap.get(curAtomChId).getResno()) < 5)
{
chainTerMap.put(curAtomChId, curAtom);
if ((curAtom.getResno() - chainTerMap.get(curAtomChId).getResno()) < 5)
{
chainTerMap.put(curAtomChId, curAtom);