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Merge branch 'develop' into bug/JAL-4289_group_boundary_not_drawn_properly_in_fastpai...
[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
a276fb6
..
0ca2ba8
100644
(file)
--- a/
src/jalview/ext/jmol/JmolParser.java
+++ b/
src/jalview/ext/jmol/JmolParser.java
@@
-88,6
+88,10
@@
public class JmolParser extends StructureFile implements JmolStatusListener
super(inFile, sourceType, tempfacType);
}
super(inFile, sourceType, tempfacType);
}
+ public JmolParser(FileParse fp, boolean doXferSettings) throws IOException
+ {
+ super(fp, doXferSettings);
+ }
public JmolParser(FileParse fp) throws IOException
{
super(fp);
public JmolParser(FileParse fp) throws IOException
{
super(fp);
@@
-108,6
+112,12
@@
public class JmolParser extends StructureFile implements JmolStatusListener
@Override
public void parse() throws IOException
{
@Override
public void parse() throws IOException
{
+ parse(true);
+ }
+
+ @Override
+ public void parse(boolean doXferSettings) throws IOException
+ {
setChains(new Vector<PDBChain>());
Viewer jmolModel = getJmolData();
jmolModel.openReader(getDataName(), getDataName(), getReader());
setChains(new Vector<PDBChain>());
Viewer jmolModel = getJmolData();
jmolModel.openReader(getDataName(), getDataName(), getReader());
@@
-132,7
+142,7
@@
public class JmolParser extends StructureFile implements JmolStatusListener
? PDBEntry.Type.MMCIF.toString()
: "PDB");
? PDBEntry.Type.MMCIF.toString()
: "PDB");
- transformJmolModelToJalview(jmolModel.ms);
+ transformJmolModelToJalview(jmolModel.ms, doXferSettings);
}
}
}
}
@@
-202,7
+212,8
@@
public class JmolParser extends StructureFile implements JmolStatusListener
return false;
}
return false;
}
- public void transformJmolModelToJalview(ModelSet ms) throws IOException
+ public void transformJmolModelToJalview(ModelSet ms,
+ boolean localDoXferSettings) throws IOException
{
try
{
{
try
{
@@
-260,7
+271,7
@@
public class JmolParser extends StructureFile implements JmolStatusListener
}
lastID = tmpatom.resNumIns.trim();
}
}
lastID = tmpatom.resNumIns.trim();
}
- if (isParseImmediately())
+ if (isParseImmediately() && localDoXferSettings)
{
// configure parsing settings from the static singleton
xferSettings();
{
// configure parsing settings from the static singleton
xferSettings();
@@
-292,7
+303,7
@@
public class JmolParser extends StructureFile implements JmolStatusListener
{
try
{
{
try
{
- Console.info("retrieving pAE for " + pdbId);
+ Console.info("Retrieving PAE for " + pdbId);
File paeFile = EBIAlfaFold.fetchAlphaFoldPAE(pdbId, null);
this.setPAEMatrix(paeFile.getAbsolutePath());
} catch (Throwable t)
File paeFile = EBIAlfaFold.fetchAlphaFoldPAE(pdbId, null);
this.setPAEMatrix(paeFile.getAbsolutePath());
} catch (Throwable t)
@@
-303,21
+314,31
@@
public class JmolParser extends StructureFile implements JmolStatusListener
// add a PAEMatrix if set (either by above or otherwise)
if (hasPAEMatrix())
{
// add a PAEMatrix if set (either by above or otherwise)
if (hasPAEMatrix())
{
- Alignment al = new Alignment(prot.toArray(new SequenceI[0]));
- EBIAlfaFold.addAlphaFoldPAE(al, new File(this.getPAEMatrix()), 0,
- null, false, false, null);
-
- if (al.getAlignmentAnnotation() != null)
+ try
{
{
- for (AlignmentAnnotation alann : al.getAlignmentAnnotation())
+ Alignment al = new Alignment(prot.toArray(new SequenceI[0]));
+ EBIAlfaFold.addAlphaFoldPAE(al, new File(this.getPAEMatrix()), 0,
+ null, false, false, null);
+
+ if (al.getAlignmentAnnotation() != null)
{
{
- annotations.add(alann);
+ for (AlignmentAnnotation alann : al.getAlignmentAnnotation())
+ {
+ annotations.add(alann);
+ }
}
}
+ } catch (Throwable ff)
+ {
+ Console.error("Couldn't import PAE Matrix from " + getPAEMatrix(),
+ ff);
+ warningMessage += "Couldn't import PAE Matrix"
+ + getNewlineString() + ff.getLocalizedMessage()
+ + getNewlineString();
}
}
} catch (OutOfMemoryError er)
{
}
}
} catch (OutOfMemoryError er)
{
- System.out.println(
+ jalview.bin.Console.outPrintln(
"OUT OF MEMORY LOADING TRANSFORMING JMOL MODEL TO JALVIEW MODEL");
throw new IOException(MessageManager
.getString("exception.outofmemory_loading_mmcif_file"));
"OUT OF MEMORY LOADING TRANSFORMING JMOL MODEL TO JALVIEW MODEL");
throw new IOException(MessageManager
.getString("exception.outofmemory_loading_mmcif_file"));
@@
-370,7
+391,7
@@
public class JmolParser extends StructureFile implements JmolStatusListener
org.jmol.modelset.Atom prevAtom,
HashMap<String, org.jmol.modelset.Atom> chainTerMap)
{
org.jmol.modelset.Atom prevAtom,
HashMap<String, org.jmol.modelset.Atom> chainTerMap)
{
- // System.out.println("Atom: " + curAtom.getAtomNumber()
+ // jalview.bin.Console.outPrintln("Atom: " + curAtom.getAtomNumber()
// + " Last atom index " + curAtom.group.lastAtomIndex);
if (chainTerMap == null || prevAtom == null)
{
// + " Last atom index " + curAtom.group.lastAtomIndex);
if (chainTerMap == null || prevAtom == null)
{
@@
-467,7
+488,7
@@
public class JmolParser extends StructureFile implements JmolStatusListener
{
int length = sq.getLength();
boolean ssFound = false;
{
int length = sq.getLength();
boolean ssFound = false;
- Annotation asecstr[] = new Annotation[length + firstResNum - 1];
+ Annotation asecstr[] = new Annotation[length + (firstResNum-sq.getStart())];
for (int p = 0; p < length; p++)
{
if (secstr[p] >= 'A' && secstr[p] <= 'z')
for (int p = 0; p < length; p++)
{
if (secstr[p] >= 'A' && secstr[p] <= 'z')