From b46275c83e658850adedf791696f3453aa1f9cb0 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@dundee.ac.uk>
Date: Fri, 15 Nov 2024 11:27:09 +0000
Subject: [PATCH] JAL-3914 infer TFType from the 3d-beacons metadata, and
 store/restore TFType in PDBEntry

---
 src/jalview/datamodel/PDBEntry.java                |   78 ++++++++++++++++++++
 .../ThreeDBStructureChooserQuerySource.java        |   40 ++++++++++
 2 files changed, 118 insertions(+)

diff --git a/src/jalview/datamodel/PDBEntry.java b/src/jalview/datamodel/PDBEntry.java
index b6b13c9..9246744 100755
--- a/src/jalview/datamodel/PDBEntry.java
+++ b/src/jalview/datamodel/PDBEntry.java
@@ -25,6 +25,7 @@ import java.util.Enumeration;
 import java.util.Hashtable;
 
 import jalview.io.StructureFile;
+import jalview.structure.StructureImportSettings.TFType;
 import jalview.util.CaseInsensitiveString;
 
 public class PDBEntry
@@ -562,6 +563,15 @@ public class PDBEntry
 
   private static final String PROVIDERCATEGORY = "PROVIDERCATEGORY";
 
+  private static final String TEMPFACTYPE = "TEMPFACTYPE";
+
+  private static final String MODELCONFIDENCE = "MODELCONFIDENCE";
+
+  private static final String MODELCONFTYPE = "MODELCONFTYPE";
+
+  private static final String MODELCONFVER = "MODELCONFVER";
+
+  
   /**
    * Permanent URI for retrieving the original structure data
    * 
@@ -662,4 +672,72 @@ public class PDBEntry
     return _hasProperty(PROVIDERCATEGORY);
   }
 
+  public void setTempFacType(TFType tempfactype)
+  {
+    setProperty(TEMPFACTYPE, tempfactype);
+  }
+
+  /**
+   * String version of TFType enum
+   * @return
+   */
+  public String getTempFacType()
+  {
+    return (String) getProperty(TEMPFACTYPE);
+  }
+  public TFType getTempFacTypeTFType()
+  {
+    return TFType.valueOf((String) getProperty(TEMPFACTYPE));
+  }
+
+  public boolean hasTempFacType()
+  {
+    return _hasProperty(TEMPFACTYPE);
+  }
+
+  public void setModelConfidenceType(String modelConfType2)
+  {
+    setProperty(MODELCONFTYPE, modelConfType2);
+  }
+
+  public boolean hasModelConfidenceType()
+  {
+    return _hasProperty(MODELCONFTYPE);
+  }
+
+  public String getModelConfidenceType()
+  {
+    return (String) getProperty(MODELCONFTYPE);
+  }
+
+  public void setModelConfidenceVersion(String modelConfVer2)
+  {
+    setProperty(MODELCONFVER, modelConfVer2);
+  }
+
+  public boolean hasModelConfidenceVersion()
+  {
+    return _hasProperty(MODELCONFVER);
+  }
+
+  public String getModelConfidenceVersion()
+  {
+    return (String) getProperty(MODELCONFVER);
+  }
+
+  public void setModelConfidence(Double modelConf)
+  {
+    setProperty(MODELCONFIDENCE, modelConf);
+  }
+
+  public boolean hasModelConfidence()
+  {
+    return _hasProperty(MODELCONFIDENCE);
+  }
+
+  public Double getModelConfidence()
+  {
+    return (Double) getProperty(MODELCONFIDENCE);
+  }
+
 }
diff --git a/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java b/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
index 2bd5a91..5c0d425 100644
--- a/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
+++ b/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
@@ -47,6 +47,7 @@ import jalview.fts.core.FTSRestResponse;
 import jalview.fts.service.threedbeacons.TDB_FTSData;
 import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient;
 import jalview.jbgui.FilterOption;
+import jalview.structure.StructureImportSettings.TFType;
 
 /**
  * logic for querying the 3DBeacons API for structures of sequences
@@ -388,6 +389,11 @@ public class ThreeDBStructureChooserQuerySource
     int humanUrl = restable.getColumn("Page URL").getModelIndex();
     int modelformat = restable.getColumn("Model Format").getModelIndex();
     int idx_mcat = restable.getColumn("Model Category").getModelIndex();
+    int idx_mqual = restable.getColumn("Confidence").getModelIndex();
+    int idx_mqualtype = restable.getColumn("Confidence Score Type").getModelIndex();
+    int idx_mqualtypever = restable.getColumn("Confidence Score Version").getModelIndex();
+    
+   
 
     final int up_start_idx = restable.getColumn("Uniprot Start")
             .getModelIndex();
@@ -429,6 +435,29 @@ public class ThreeDBStructureChooserQuerySource
       String modelCategory = idx_mcat < 1 ? null
               : (String) restable.getValueAt(row, idx_mcat);
 
+      
+      Double modelConf = idx_mqual < 1 ? null
+              : (Double) restable.getValueAt(row, idx_mqual);
+      
+      String modelConfType = idx_mqualtype < 1 ? null
+              : (String) restable.getValueAt(row, idx_mqualtype);
+      String modelConfVer = idx_mqualtypever < 1 ? null
+              : (String) restable.getValueAt(row, idx_mqualtypever);
+      
+      String tftype = modelConfType.toUpperCase(Locale.ROOT);
+      TFType tempfacType = (tftype==null) ? null : TFType.valueOf(tftype);
+      if (tftype==null || "".equals(tftype) || TFType.valueOf(tftype) == null )
+      {
+        // TODO maintain mappings between confidence types and tempfactypes
+        if (typeColumn.toLowerCase(Locale.ROOT).startsWith("alpha") || tftype.startsWith("ALPHAFOLD")) {
+          tftype = TFType.PLDDT.toString();
+          modelConfVer = null;
+        }
+        if (!typeColumn.toLowerCase(Locale.ROOT).startsWith("pdbe")) {
+          tftype = TFType.QMEANDISCO.toString();
+        }
+      }
+           
       String strucFormat = restable.getValueAt(row, modelformat).toString();
 
       SequenceI selectedSeq = (SequenceI) restable.getValueAt(row,
@@ -464,6 +493,17 @@ public class ThreeDBStructureChooserQuerySource
           pdbEntry.setProviderPage(modelPage);
         }
         pdbEntry.setProviderCategory(modelCategory);
+        pdbEntry.setTempFacType(tempfacType);
+        if (modelConf != null) {
+          pdbEntry.setModelConfidence(modelConf);
+        }
+        if (modelConfType != null) {
+          pdbEntry.setModelConfidenceType(modelConfType);
+        }
+        if (modelConfVer != null) {
+          pdbEntry.setModelConfidenceVersion(modelConfVer);
+        }
+        
         selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
       }
       pdbEntriesToView[count++] = pdbEntry;
-- 
1.7.10.2