Merge branch 'develop' into features/JAL-4134_use_annotation_row_for_colours_and_groups

[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 37b3d68..c64dac1 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;
@@ -67,8 +68,6 @@ public class JmolParser extends StructureFile implements JmolStatusListener
 {
   Viewer viewer = null;
 
-  private boolean alphaFoldModel;
-
   public JmolParser(boolean immediate, Object inFile,
           DataSourceType sourceType) throws IOException
   {
@@ -89,6 +88,10 @@ public class JmolParser extends StructureFile implements JmolStatusListener
     super(inFile, sourceType, tempfacType);
   }
 
+  public JmolParser(FileParse fp, boolean doXferSettings) throws IOException
+  {
+    super(fp, doXferSettings);
+  }
   public JmolParser(FileParse fp) throws IOException
   {
     super(fp);
@@ -109,6 +112,12 @@ public class JmolParser extends StructureFile implements JmolStatusListener
   @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());
@@ -133,7 +142,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
                       ? PDBEntry.Type.MMCIF.toString()
                       : "PDB");
 
-      transformJmolModelToJalview(jmolModel.ms);
+      transformJmolModelToJalview(jmolModel.ms, doXferSettings);
     }
   }
 
@@ -203,7 +212,8 @@ public class JmolParser extends StructureFile implements JmolStatusListener
     return false;
   }
 
-  public void transformJmolModelToJalview(ModelSet ms) throws IOException
+  public void transformJmolModelToJalview(ModelSet ms,
+          boolean localDoXferSettings) throws IOException
   {
     try
     {
@@ -231,8 +241,7 @@ 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)
@@ -250,9 +259,8 @@ public class JmolParser extends StructureFile implements JmolStatusListener
         else
         {
           AnnotationRowBuilder builder = null;
-          String tempFString = null;
-          if (isAlphafoldModel() || this
-                  .getTemperatureFactorType() == StructureImportSettings.TFType.PLDDT)
+          if (isAlphafoldModel()
+                  || getTemperatureFactorType() == StructureImportSettings.TFType.PLDDT)
           {
             builder = new AlphaFoldAnnotationRowBuilder();
           }
@@ -263,7 +271,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
         }
         lastID = tmpatom.resNumIns.trim();
       }
-      if (isParseImmediately())
+      if (isParseImmediately() && localDoXferSettings)
       {
         // configure parsing settings from the static singleton
         xferSettings();
@@ -290,15 +298,28 @@ public class JmolParser extends StructureFile implements JmolStatusListener
           createAnnotation(chainseq, chain, ms.at);
         }
       }
-      if (isAlphafoldModel())
+      // 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())
       {
-        // TODO - work out how to handle different ways that pAE is provided
-        //
         try
         {
-          Console.info("retrieving pAE for " + pdbId);
           Alignment al = new Alignment(prot.toArray(new SequenceI[0]));
-          EBIAlfaFold.retrieve_AlphaFold_pAE(pdbId, al, null);
+          EBIAlfaFold.addAlphaFoldPAE(al, new File(this.getPAEMatrix()), 0,
+                  null, false, false, null);
+
           if (al.getAlignmentAnnotation() != null)
           {
             for (AlignmentAnnotation alann : al.getAlignmentAnnotation())
@@ -306,10 +327,13 @@ public class JmolParser extends StructureFile implements JmolStatusListener
               annotations.add(alann);
             }
           }
-          ;
-        } catch (Throwable t)
+        } catch (Throwable ff)
         {
-          Console.error("Couldn't get the pAE for " + pdbId, t);
+          Console.error("Couldn't import PAE Matrix from " + getPAEMatrix(),
+                  ff);
+          warningMessage += "Couldn't import PAE Matrix"
+                  + getNewlineString() + ff.getLocalizedMessage()
+                  + getNewlineString();
         }
       }
     } catch (OutOfMemoryError er)
@@ -321,16 +345,6 @@ public class JmolParser extends StructureFile implements JmolStatusListener
     }
   }
 
-  public void setAlphafoldModel(boolean afm)
-  {
-    alphaFoldModel = afm;
-  }
-
-  private boolean isAlphafoldModel()
-  {
-    return alphaFoldModel;
-  }
-
   private List<Atom> convertSignificantAtoms(ModelSet ms)
   {
     List<Atom> significantAtoms = new ArrayList<Atom>();