JAL-629 Attempts to add PAE to structure. --headless working. Make HTML output single...

[jalview.git] / src / jalview / ws / dbsources / EBIAlfaFold.java

diff --git a/src/jalview/ws/dbsources/EBIAlfaFold.java b/src/jalview/ws/dbsources/EBIAlfaFold.java
index 859ac05..e5f1243 100644 (file)
--- a/src/jalview/ws/dbsources/EBIAlfaFold.java
+++ b/src/jalview/ws/dbsources/EBIAlfaFold.java
@@ -36,6 +36,7 @@ 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;
@@ -49,6 +50,7 @@ import jalview.io.FileFormat;
 import jalview.io.FileFormatI;
 import jalview.io.FormatAdapter;
 import jalview.io.PDBFeatureSettings;
+import jalview.structure.StructureMapping;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
@@ -257,48 +259,85 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
   public static void addAlphaFoldPAEToSequence(AlignmentI pdbAlignment,
           File pae, int index, String seqId)
   {
-    FileInputStream pae_input = null;
+    addAlphaFoldPAE(pdbAlignment, pae, index, seqId, false, false);
+  }
+
+  public static void addAlphaFoldPAEToStructure(AlignmentI pdbAlignment,
+          File pae, int index, String structIdOrFile, boolean isStructId)
+  {
+    addAlphaFoldPAE(pdbAlignment, pae, index, structIdOrFile, true,
+            isStructId);
+  }
+
+  public static void addAlphaFoldPAE(AlignmentI pdbAlignment, File pae,
+          int index, String id, boolean isStruct, boolean isStructId)
+  {
+    FileInputStream paeInput = null;
     try
     {
-      pae_input = new FileInputStream(pae);
+      paeInput = new FileInputStream(pae);
     } catch (FileNotFoundException e)
     {
       Console.error(
               "Could not find pAE file '" + pae.getAbsolutePath() + "'", e);
+      return;
     }
 
-    try
+    if (isStruct)
     {
-      if (!importPaeJSONAsContactMatrix(pdbAlignment, pae_input, index,
-              seqId))
+      StructureSelectionManager ssm = StructureSelectionManager
+              .getStructureSelectionManager(Desktop.instance);
+      if (ssm != null)
       {
-        Console.warn("Could not import contact matrix from '"
-                + pae.getAbsolutePath() + "'");
-      }
-    } catch (IOException e1)
-    {
-      Console.error("Error when importing pAE file '"
-              + pae.getAbsolutePath() + "'", e1);
-    } catch (ParseException e2)
-    {
-      Console.error(
-              "Error when parsing pAE file '" + pae.getAbsolutePath() + "'",
-              e2);
-    }
+        String structFile = isStructId ? ssm.findFileForPDBId(id) : id;
+        Console.debug("##### AHA! structFile = " + structFile);
+        Console.debug("##### structFile "
+                + (ssm.isPDBFileRegistered(structFile) ? "IS " : "is NOT ")
+                + "registered.");
 
-  }
+        StructureMapping[] smArray = ssm.getMapping(structFile);
+        Console.debug("##### AHA! smArray obtained with " + smArray.length
+                + " elements");
 
-  public static void addAlphaFoldPAEToStructure(AlignmentI pdbAlignment,
-          File pae, int index, String structId)
-  {
-    StructureSelectionManager ssm = StructureSelectionManager
-            .getStructureSelectionManager(Desktop.instance);
-    if (ssm != null)
+        try
+        {
+          if (!importPaeJSONAsContactMatrixToStructure(smArray, paeInput))
+          {
+            Console.warn("Could not import contact matrix from '"
+                    + pae.getAbsolutePath() + "' to structure.");
+          }
+        } catch (IOException e1)
+        {
+          Console.error("Error when importing pAE file '"
+                  + pae.getAbsolutePath() + "'", e1);
+        } catch (ParseException e2)
+        {
+          Console.error("Error when parsing pAE file '"
+                  + pae.getAbsolutePath() + "'", e2);
+        }
+      }
+
+    }
+    else
     {
-      /*
-      ssm.setAddTempFacAnnot(showTemperatureFactor);
-      ssm.setProcessSecondaryStructure(showSecondaryStructure);
-      */
+      // attach to sequence?!
+      try
+      {
+        if (!importPaeJSONAsContactMatrixToSequence(pdbAlignment, paeInput,
+                index, id))
+        {
+          Console.warn("Could not import contact matrix from '"
+                  + pae.getAbsolutePath() + "' to sequence.");
+        }
+      } catch (IOException e1)
+      {
+        Console.error("Error when importing pAE file '"
+                + pae.getAbsolutePath() + "'", e1);
+      } catch (ParseException e2)
+      {
+        Console.error("Error when parsing pAE file '"
+                + pae.getAbsolutePath() + "'", e2);
+      }
     }
 
   }
@@ -314,24 +353,18 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
    * @throws IOException
    * @throws Exception
    */
-  public static boolean importPaeJSONAsContactMatrix(
+  public static boolean importPaeJSONAsContactMatrixToSequence(
           AlignmentI pdbAlignment, InputStream pae_input)
           throws IOException, ParseException
   {
-    return importPaeJSONAsContactMatrix(pdbAlignment, pae_input, 0, null);
+    return importPaeJSONAsContactMatrixToSequence(pdbAlignment, pae_input,
+            0, null);
   }
 
-  public static boolean importPaeJSONAsContactMatrix(
+  public static boolean importPaeJSONAsContactMatrixToSequence(
           AlignmentI pdbAlignment, InputStream pae_input, int index,
           String seqId) throws IOException, ParseException
   {
-
-    List<Object> pae_obj = (List<Object>) Platform.parseJSON(pae_input);
-    if (pae_obj == null)
-    {
-      Console.debug("JSON file did not parse properly.");
-      return false;
-    }
     SequenceI sequence = null;
     /* debugging */
     SequenceI[] seqs = pdbAlignment.getSequencesArray();
@@ -369,6 +402,13 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
         sequence = sequences[0]; // just use the first sequence with this seqId
       }
     }
+
+    List<Object> pae_obj = (List<Object>) Platform.parseJSON(pae_input);
+    if (pae_obj == null)
+    {
+      Console.debug("JSON file did not parse properly.");
+      return false;
+    }
     ContactMatrixI matrix = new PAEContactMatrix(sequence,
             (Map<String, Object>) pae_obj.get(0));
 
@@ -377,6 +417,50 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
     return true;
   }
 
+  public static boolean importPaeJSONAsContactMatrixToStructure(
+          StructureMapping[] smArray, InputStream paeInput)
+          throws IOException, ParseException
+  {
+    boolean someDone = false;
+    Console.debug("##### smArray.length=" + smArray.length);
+    for (StructureMapping sm : smArray)
+    {
+      Console.debug("##### sm[n]=" + sm.getPdbId());
+      boolean thisDone = importPaeJSONAsContactMatrixToStructure(sm,
+              paeInput);
+      Console.debug("##### thisDone = " + thisDone);
+      someDone |= thisDone;
+    }
+    return someDone;
+  }
+
+  public static boolean importPaeJSONAsContactMatrixToStructure(
+          StructureMapping sm, InputStream paeInput)
+          throws IOException, ParseException
+  {
+
+    List<Object> pae_obj = (List<Object>) Platform.parseJSON(paeInput);
+    if (pae_obj == null)
+    {
+      Console.debug("JSON file did not parse properly.");
+      return false;
+    }
+
+    ContactMatrixI matrix = new PAEContactMatrix(sm.getSequence(),
+            (Map<String, Object>) pae_obj.get(0));
+
+    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();
+
+    return true;
+  }
+
   /**
    * general purpose structure importer - designed to yield alignment useful for
    * transfer of annotation to associated sequences