JAL-629 Removal of unnecessary methods. Set pLTTD tempfac for EBIAlfafold. Simplify...

[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 05c3f7a..f0e477c 100644 (file)
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -20,6 +20,7 @@
  */
 package jalview.ext.jmol;
 
+import java.io.File;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.HashMap;
@@ -37,18 +38,22 @@ import org.jmol.viewer.Viewer;
 
 import com.stevesoft.pat.Regex;
 
+import jalview.bin.Console;
+import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
-import jalview.datamodel.annotations.AnnotationRowBuilder.AlphaFoldAnnotationRowBuilder;
-import jalview.datamodel.annotations.AnnotationRowBuilder.AnnotationRowBuilder;
+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.structure.StructureImportSettings;
 import jalview.util.Format;
 import jalview.util.MessageManager;
+import jalview.ws.dbsources.EBIAlfaFold;
 import mc_view.Atom;
 import mc_view.PDBChain;
 import mc_view.Residue;
@@ -63,19 +68,24 @@ public class JmolParser extends StructureFile implements JmolStatusListener
 {
   Viewer viewer = null;
 
-  private boolean alphaFoldModel;
-
   public JmolParser(boolean immediate, Object inFile,
           DataSourceType sourceType) throws IOException
   {
     // BH 2018 File or String for filename
     super(immediate, inFile, sourceType);
+
   }
 
   public JmolParser(Object inFile, DataSourceType sourceType)
           throws IOException
   {
-    super(inFile, sourceType);
+    this(inFile, sourceType, null);
+  }
+
+  public JmolParser(Object inFile, DataSourceType sourceType,
+          StructureImportSettings.TFType tempfacType) throws IOException
+  {
+    super(inFile, sourceType, tempfacType);
   }
 
   public JmolParser(FileParse fp) throws IOException
@@ -220,8 +230,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
       {
         setId(pdbId);
         setPDBIdAvailable(true);
-        alphaFoldModel = alphaFold.search(pdbId) && isMMCIF;
-
+        setAlphafoldModel(alphaFold.search(pdbId) && isMMCIF);
       }
       List<Atom> significantAtoms = convertSignificantAtoms(ms);
       for (Atom tmpatom : significantAtoms)
@@ -239,8 +248,8 @@ public class JmolParser extends StructureFile implements JmolStatusListener
         else
         {
           AnnotationRowBuilder builder = null;
-          String tempFString = null;
-          if (isAlphafoldModel())
+          if (isAlphafoldModel()
+                  || getTemperatureFactorType() == StructureImportSettings.TFType.PLDDT)
           {
             builder = new AlphaFoldAnnotationRowBuilder();
           }
@@ -278,6 +287,34 @@ public class JmolParser extends StructureFile implements JmolStatusListener
           createAnnotation(chainseq, chain, ms.at);
         }
       }
+      // if Alphafold, fetch the PAE matrix if doesn't already have one
+      if (isAlphafoldModel() && !hasPAEMatrix())
+      {
+        try
+        {
+          Console.info("retrieving pAE for " + pdbId);
+          File paeFile = EBIAlfaFold.fetchAlphaFoldPAE(pdbId, null);
+          this.setPAEMatrix(paeFile.getAbsolutePath());
+        } catch (Throwable t)
+        {
+          Console.error("Couldn't get the pAE for " + pdbId, t);
+        }
+      }
+      // 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);
+
+        if (al.getAlignmentAnnotation() != null)
+        {
+          for (AlignmentAnnotation alann : al.getAlignmentAnnotation())
+          {
+            annotations.add(alann);
+          }
+        }
+      }
     } catch (OutOfMemoryError er)
     {
       System.out.println(
@@ -287,11 +324,6 @@ public class JmolParser extends StructureFile implements JmolStatusListener
     }
   }
 
-  private boolean isAlphafoldModel()
-  {
-    return alphaFoldModel;
-  }
-
   private List<Atom> convertSignificantAtoms(ModelSet ms)
   {
     List<Atom> significantAtoms = new ArrayList<Atom>();
@@ -442,8 +474,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
       {
         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)
         {