JAL-629 improvements to argparser toString. Improvements to cli paeFile structure...

[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 aba0d4b..5165d04 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;
@@ -199,6 +199,7 @@ 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());
@@ -293,11 +294,12 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
           AlignmentI pdbAlignment, String retrievalUrl) throws IOException
   {
     File pae = fetchAlphaFoldPAE(id, retrievalUrl);
-    addAlphaFoldPAE(pdbAlignment, pae, 0, null, false, false);
+    addAlphaFoldPAE(pdbAlignment, pae, 0, null, false, false, null);
   }
 
   public static void addAlphaFoldPAE(AlignmentI pdbAlignment, File pae,
-          int index, String id, boolean isStruct, boolean isStructId)
+          int index, String id, boolean isStruct, boolean isStructId,
+          String label)
   {
     FileInputStream paeInput = null;
     try
@@ -317,7 +319,7 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
       if (ssm != null)
       {
         String structFilename = isStructId ? ssm.findFileForPDBId(id) : id;
-        addPAEToStructure(ssm, structFilename, pae);
+        addPAEToStructure(ssm, structFilename, pae, label);
       }
 
     }
@@ -327,7 +329,7 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
       try
       {
         if (!importPaeJSONAsContactMatrixToSequence(pdbAlignment, paeInput,
-                index, id))
+                index, id, label))
         {
           Console.warn("Could not import contact matrix from '"
                   + pae.getAbsolutePath() + "' to sequence.");
@@ -346,7 +348,7 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
   }
 
   public static void addPAEToStructure(StructureSelectionManager ssm,
-          String structFilename, File pae)
+          String structFilename, File pae, String label)
   {
     FileInputStream paeInput = null;
     try
@@ -369,7 +371,8 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
 
       try
       {
-        if (!importPaeJSONAsContactMatrixToStructure(smArray, paeInput))
+        if (!importPaeJSONAsContactMatrixToStructure(smArray, paeInput,
+                label))
         {
           Console.warn("Could not import contact matrix from '"
                   + pae.getAbsolutePath() + "' to structure.");
@@ -398,24 +401,8 @@ 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
+          String seqId, String label) throws IOException, ParseException
   {
     SequenceI sequence = null;
     if (seqId == null)
@@ -442,20 +429,13 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
       return false;
     }
     return importPaeJSONAsContactMatrixToSequence(pdbAlignment, pae_input,
-            sequence);
-  }
-
-  public static boolean importPaeJSONAsContactMatrixToSequence(
-          AlignmentI pdbAlignment, File pae_input, SequenceI sequence)
-          throws IOException, ParseException
-  {
-    return importPaeJSONAsContactMatrixToSequence(pdbAlignment,
-            new FileInputStream(pae_input), sequence);
+            sequence, label);
   }
 
   public static boolean importPaeJSONAsContactMatrixToSequence(
           AlignmentI pdbAlignment, InputStream pae_input,
-          SequenceI sequence) throws IOException, ParseException
+          SequenceI sequence, String label)
+          throws IOException, ParseException
   {
     JSONObject paeDict = parseJSONtoPAEContactMatrix(pae_input);
     if (paeDict == null)
@@ -467,6 +447,8 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
             (Map<String, Object>) paeDict);
 
     AlignmentAnnotation cmannot = sequence.addContactList(matrix);
+    if (label != null)
+      cmannot.label = label;
     pdbAlignment.addAnnotation(cmannot);
 
     return true;
@@ -492,21 +474,21 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
   }
 
   public static boolean importPaeJSONAsContactMatrixToStructure(
-          StructureMapping[] smArray, InputStream paeInput)
+          StructureMapping[] smArray, InputStream paeInput, String label)
           throws IOException, ParseException
   {
     boolean someDone = false;
     for (StructureMapping sm : smArray)
     {
       boolean thisDone = importPaeJSONAsContactMatrixToStructure(sm,
-              paeInput);
+              paeInput, label);
       someDone |= thisDone;
     }
     return someDone;
   }
 
   public static boolean importPaeJSONAsContactMatrixToStructure(
-          StructureMapping sm, InputStream paeInput)
+          StructureMapping sm, InputStream paeInput, String label)
           throws IOException, ParseException
   {
     JSONObject pae_obj = parseJSONtoPAEContactMatrix(paeInput);
@@ -520,13 +502,12 @@ 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();
+    if (label != null)
+    {
+      Console.debug("Setting annotation label to '" + label + "'");
+      cmannot.label = label;
+    }
+    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)