*/
package jalview.ext.jmol;
-import jalview.datamodel.AlignmentAnnotation;
-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.util.Format;
-import jalview.util.MessageManager;
-
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
import java.util.Vector;
import com.stevesoft.pat.Regex;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.annotations.AlphaFoldAnnotationRowBuilder;
+import jalview.datamodel.annotations.AnnotationRowBuilder;
+import jalview.io.DataSourceType;
+import jalview.io.FileParse;
+import jalview.io.StructureFile;
+import jalview.schemes.ResidueProperties;
+import jalview.util.Format;
+import jalview.util.MessageManager;
import mc_view.Atom;
import mc_view.PDBChain;
import mc_view.Residue;
// }
// ;
// instead, we distinguish .cif from non-.cif by filename
- setStructureFileType(getDataName().toLowerCase().endsWith(".cif")
- ? PDBEntry.Type.MMCIF.toString()
- : "PDB");
+ setStructureFileType(
+ getDataName().toLowerCase(Locale.ROOT).endsWith(".cif")
+ ? PDBEntry.Type.MMCIF.toString()
+ : "PDB");
transformJmolModelToJalview(jmolModel.ms);
}
* params -o (output to sysout) -n (nodisplay) -x (exit when finished)
* see http://wiki.jmol.org/index.php/Jmol_Application
*/
-
+
viewer = JalviewJmolBinding.getJmolData(this);
// ensure the 'new' (DSSP) not 'old' (Ramachandran) SS method is used
viewer.setBooleanProperty("defaultStructureDSSP", true);
}
return viewer;
}
-
+
public static Regex getNewAlphafoldValidator()
{
- Regex validator = new Regex("(AF-[A-Z]+[0-9]+[A-Z0-9]+-F1)");
+ Regex validator = new Regex("(AF-[A-Z]+[0-9]+[A-Z0-9]+-F1)");
validator.setIgnoreCase(true);
return validator;
}
- PDBEntry.Type jmolFiletype=null;
+ PDBEntry.Type jmolFiletype = null;
+
/**
- * resolve a jmol filetype string and update the jmolFiletype field accordingly
+ * resolve a jmol filetype string and update the jmolFiletype field
+ * accordingly
+ *
* @param jmolIdentifiedFileType
* @return true if filetype was identified as MMCIF, PDB
*/
public boolean updateFileType(String jmolIdentifiedFileType)
{
- if (jmolIdentifiedFileType == null
+ if (jmolIdentifiedFileType == null
|| jmolIdentifiedFileType.trim().equals(""))
{
return false;
}
- if ("mmcif".equalsIgnoreCase(jmolIdentifiedFileType)) {
+ if ("mmcif".equalsIgnoreCase(jmolIdentifiedFileType))
+ {
jmolFiletype = PDBEntry.Type.MMCIF;
return true;
}
{
jmolFiletype = PDBEntry.Type.PDB;
return true;
- }
+ }
return false;
}
-
+
public void transformJmolModelToJalview(ModelSet ms) throws IOException
{
try
{
setStructureFileType(jmolFiletype.toString());
}
-
+
isMMCIF = PDBEntry.Type.MMCIF.equals(jmolFiletype);
-
+
if (pdbId == null)
{
setId(safeName(getDataName()));
{
setId(pdbId);
setPDBIdAvailable(true);
- alphaFoldModel = alphaFold.search(pdbId) && isMMCIF;
+ alphaFoldModel = alphaFold.search(pdbId) && isMMCIF;
}
List<Atom> significantAtoms = convertSignificantAtoms(ms);
if (tmpchain != null)
{
tmpchain.atoms.addElement(tmpatom);
- } else
+ }
+ else
{
- String tempFString=null;
+ AnnotationRowBuilder builder = null;
+ String tempFString = null;
if (isAlphafoldModel())
{
- tempFString = "Alphafold Reliability";
+ builder = new AlphaFoldAnnotationRowBuilder();
}
- tmpchain = new PDBChain(getId(), tmpatom.chain,tempFString);
+ tmpchain = new PDBChain(getId(), tmpatom.chain, builder);
getChains().add(tmpchain);
tmpchain.atoms.addElement(tmpatom);
}
{
try
{
- asecstr[p] = new Annotation(String.valueOf(secstr[p]), null,
- secstrcode[p], Float.NaN);
+ asecstr[p] = new Annotation(null, null, secstrcode[p], Float.NaN);
ssFound = true;
} catch (Exception e)
{