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

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 7142b48..271454a 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -1446,7 +1446,6 @@ warning.wrong_jvm_version_message = The Java version being used (Java {0}) may l
 label.alphafold_reliability = Alphafold Reliability
 label.tftype_default = Default
 label.tftype_plddt = pLDDT
-label.tftype_dose = Dose
 label.optional = (optional)
 label.choose_tempfac_type = Choose Temperature Factor type
 label.add_pae_matrix_file = Add PAE matrix file

diff --git a/resources/lang/Messages_es.properties b/resources/lang/Messages_es.properties
index 4b3da75..c427104 100644 (file)
--- a/resources/lang/Messages_es.properties
+++ b/resources/lang/Messages_es.properties
@@ -1432,6 +1432,5 @@ label.alphafold_reliability = Fiabilidad Alphafold
 label.optional = (opcional)
 label.tftype_default = Default
 label.tftype_plddt = pLDDT
-label.tftype_dose = Dose
 label.add_pae_matrix_file = Añadir un fichero de matriz PAE
 label.nothing_selected = Nada seleccionado

diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java
index 969d195..f0e477c 100644 (file)
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -230,9 +230,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
       {
         setId(pdbId);
         setPDBIdAvailable(true);
-        Console.debug("##### DATASOURCETYPE=" + getDataSourceType());
-        setAlphafoldModel(alphaFold.search(pdbId) && isMMCIF
-                && getDataSourceType() == DataSourceType.URL);
+        setAlphafoldModel(alphaFold.search(pdbId) && isMMCIF);
       }
       List<Atom> significantAtoms = convertSignificantAtoms(ms);
       for (Atom tmpatom : significantAtoms)
@@ -303,31 +301,16 @@ public class JmolParser extends StructureFile implements JmolStatusListener
         }
       }
       // add a PAEMatrix if set (either by above or otherwise)
-      Console.debug("##### hasPAEMatrix()=" + hasPAEMatrix());
-      Console.debug("##### isAlphafoldModel()=" + isAlphafoldModel());
-      Console.debug("##### getPAEMatrix()=" + getPAEMatrix());
       if (hasPAEMatrix())
       {
         Alignment al = new Alignment(prot.toArray(new SequenceI[0]));
-        if (isAlphafoldModel())
-        {
-          EBIAlfaFold.addAlphaFoldPAE(al, new File(this.getPAEMatrix()), 0,
-                  null, false, false);
-        }
-        else
-        {
-          EBIAlfaFold.addPAEToStructure(null, this.getInFile(),
-                  new File(this.getPAEMatrix()));
-        }
+        EBIAlfaFold.addAlphaFoldPAE(al, new File(this.getPAEMatrix()), 0,
+                null, false, false);
 
-        Console.debug("##### al.getAlignmentAnnotation()="
-                + al.getAlignmentAnnotation());
         if (al.getAlignmentAnnotation() != null)
         {
           for (AlignmentAnnotation alann : al.getAlignmentAnnotation())
           {
-            Console.debug("##### Adding to alann" + alann.annotationId + "("
-                    + alann.getCalcId() + ")");
             annotations.add(alann);
           }
         }

diff --git a/src/jalview/gui/PymolViewer.java b/src/jalview/gui/PymolViewer.java
index 5069d93..52c253d 100644 (file)
--- a/src/jalview/gui/PymolViewer.java
+++ b/src/jalview/gui/PymolViewer.java
@@ -274,7 +274,7 @@ public class PymolViewer extends StructureViewerBase
             if (pe.hasStructureFile())
             {
               pdb = pe.getStructureFile();
-              Console.debug("##### (Re)Using StructureFile " + pdb.getId());
+              Console.debug("(Re)Using StructureFile " + pdb.getId());
             }
             else
             {

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index e2eaabd..80024d9 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -1389,10 +1389,6 @@ public class StructureChooser extends GStructureChooser
       for (SequenceI seq : sequences)
       {
         PDBEntry pdbe = pdbEntriesToView[p++];
-        Console.debug(
-                "##### pdbe=" + pdbe == null ? null : pdbe.toString());
-        Console.debug("##### pdbe.getFile()=" + pdbe == null ? null
-                : pdbe.getFile());
         if (pdbe != null && pdbe.getFile() != null)
         {
           StructureMapping[] smm = ssm.getMapping(pdbe.getFile());

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index b5ed052..9a4e982 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -167,11 +167,7 @@ public class AppletFormatAdapter
   {
 
     this.selectedFile = selectedFile;
-    if (selectedFile != null)
-    {
-      this.inFile = selectedFile.getPath();
-    }
-    this.inFile = file;
+    this.inFile = selectedFile != null ? selectedFile.getPath() : file;
     try
     {
       if (fileFormat.isStructureFile())

diff --git a/src/jalview/structure/StructureImportSettings.java b/src/jalview/structure/StructureImportSettings.java
index a50101a..22ecdc7 100644 (file)
--- a/src/jalview/structure/StructureImportSettings.java
+++ b/src/jalview/structure/StructureImportSettings.java
@@ -62,7 +62,7 @@ public class StructureImportSettings
 
   public static enum TFType
   {
-    DEFAULT, PLDDT, DOSE;
+    DEFAULT, PLDDT;
 
     @Override
     public String toString()

diff --git a/src/jalview/ws/dbsources/EBIAlfaFold.java b/src/jalview/ws/dbsources/EBIAlfaFold.java
index aba0d4b..8609046 100644 (file)
--- a/src/jalview/ws/dbsources/EBIAlfaFold.java
+++ b/src/jalview/ws/dbsources/EBIAlfaFold.java
@@ -40,7 +40,6 @@ import com.stevesoft.pat.Regex;
 
 import jalview.api.FeatureSettingsModelI;
 import jalview.bin.Console;
-import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ContactMatrixI;
@@ -54,6 +53,7 @@ import jalview.io.FileFormat;
 import jalview.io.FileFormatI;
 import jalview.io.FormatAdapter;
 import jalview.io.PDBFeatureSettings;
+import jalview.structure.StructureImportSettings.TFType;
 import jalview.structure.StructureMapping;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
@@ -154,12 +154,20 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
   @Override
   public AlignmentI getSequenceRecords(String queries) throws Exception
   {
-    return getSequenceRecords(queries, null);
+    // used by the SequenceFetcher. Put forSequencesOnly to true (don't open
+    // structure viewer later)
+    return getSequenceRecords(queries, null, true);
   }
 
   public AlignmentI getSequenceRecords(String queries, String retrievalUrl)
           throws Exception
   {
+    return getSequenceRecords(queries, retrievalUrl, false);
+  }
+
+  public AlignmentI getSequenceRecords(String queries, String retrievalUrl,
+          boolean forSequencesOnly) throws Exception
+  {
     AlignmentI pdbAlignment = null;
     String chain = null;
     String id = null;
@@ -199,6 +207,7 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
       {
         return null;
       }
+      // TODO Get the PAE file somewhere around here and remove from JmolParser
 
       pdbAlignment = importDownloadedStructureFromUrl(alphaFoldCif, tmpFile,
               id, chain, getDbSource(), getDbVersion());
@@ -217,6 +226,8 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
       stopQuery();
       throw (ex);
     }
+    // distinguish between AlphaFold cif/pdb opened as structure file or fetched
+    // as sequence/alignment
     return pdbAlignment;
   }
 
@@ -398,22 +409,6 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
    * @throws Exception
    */
   public static boolean importPaeJSONAsContactMatrixToSequence(
-          AlignmentI pdbAlignment, InputStream pae_input)
-          throws IOException, ParseException
-  {
-    return importPaeJSONAsContactMatrixToSequence(pdbAlignment, pae_input,
-            0, null);
-  }
-
-  public static boolean importPaeJSONAsContactMatrixToSequence(
-          AlignmentI pdbAlignment, File paeFile, int index, String seqId)
-          throws FileNotFoundException, IOException, ParseException
-  {
-    return importPaeJSONAsContactMatrixToSequence(pdbAlignment,
-            new FileInputStream(paeFile), index, seqId);
-  }
-
-  public static boolean importPaeJSONAsContactMatrixToSequence(
           AlignmentI pdbAlignment, InputStream pae_input, int index,
           String seqId) throws IOException, ParseException
   {
@@ -446,14 +441,6 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
   }
 
   public static boolean importPaeJSONAsContactMatrixToSequence(
-          AlignmentI pdbAlignment, File pae_input, SequenceI sequence)
-          throws IOException, ParseException
-  {
-    return importPaeJSONAsContactMatrixToSequence(pdbAlignment,
-            new FileInputStream(pae_input), sequence);
-  }
-
-  public static boolean importPaeJSONAsContactMatrixToSequence(
           AlignmentI pdbAlignment, InputStream pae_input,
           SequenceI sequence) throws IOException, ParseException
   {
@@ -520,13 +507,7 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
             (Map<String, Object>) pae_obj);
 
     AlignmentAnnotation cmannot = sm.getSequence().addContactList(matrix);
-    // sm.getSequence().addAlignmentAnnotation(cmannot);
-    sm.transfer(cmannot);
-    // return true;
-
-    StructureSelectionManager ssm = StructureSelectionManager
-            .getStructureSelectionManager(Desktop.instance);
-    List<AlignedCodonFrame> acfList = ssm.getSequenceMappings();
+    sm.getSequence().addAlignmentAnnotation(cmannot);
 
     return true;
   }
@@ -551,8 +532,10 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
     String file = tmpFile.getAbsolutePath();
     // todo get rid of Type and use FileFormatI instead?
     FileFormatI fileFormat = FileFormat.MMCif;
-    AlignmentI pdbAlignment = new FormatAdapter().readFile(tmpFile,
-            DataSourceType.FILE, fileFormat);
+    TFType tempfacType = TFType.PLDDT;
+    AlignmentI pdbAlignment = new FormatAdapter().readFile(tmpFile, file,
+            DataSourceType.FILE, fileFormat, tempfacType);
+
     if (pdbAlignment != null)
     {
       List<SequenceI> toremove = new ArrayList<SequenceI>();
@@ -565,7 +548,6 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
           if (pid.getFile() == file)
           {
             chid = pid.getChainCode();
-
           }
         }
         if (chain == null || (chid != null && (chid.equals(chain)