From 2ec1365eda085f8e21a8faa384c67c136774b599 Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Mon, 27 Feb 2023 09:47:23 +0000
Subject: [PATCH] JAL-629 removed debug prints. added .cif. added some
 comments/code-markers

---
 src/jalview/bin/Commands.java             |   14 ++++++++++++++
 src/jalview/gui/StructureChooser.java     |   20 +++++++++++++++++++-
 src/jalview/ws/dbsources/EBIAlfaFold.java |   24 ------------------------
 3 files changed, 33 insertions(+), 25 deletions(-)

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index 7a6e3ac..f8481f5 100644
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -384,6 +384,20 @@ public class Commands
             Console.debug("Using structure file (from argument) '"
                     + structureFile.getAbsolutePath() + "'");
           }
+
+          // TRY THIS
+          /*
+           PDBEntry fileEntry = new AssociatePdbFileWithSeq()
+                  .associatePdbWithSeq(selectedPdbFileName,
+                          DataSourceType.FILE, selectedSequence, true,
+                          Desktop.instance);
+                          
+           sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry },
+                  ap, new SequenceI[]
+                  { selectedSequence });
+          
+           */
+
           /* THIS DOESN'T WORK */
           else if (seq.getAllPDBEntries() != null
                   && seq.getAllPDBEntries().size() > 0)
diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 47bec31..11e50db 100644
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -725,7 +725,9 @@ public class StructureChooser extends GStructureChooser
 
   private String guessPAEFilename()
   {
-    if (selectedPdbFileName.toLowerCase(Locale.ROOT).endsWith(".pdb"))
+    if (selectedPdbFileName.toLowerCase(Locale.ROOT).endsWith(".pdb")
+            || selectedPdbFileName.toLowerCase(Locale.ROOT)
+                    .endsWith(".cif"))
     {
       String jsonExt = selectedPdbFileName.substring(0,
               selectedPdbFileName.length() - 4) + ".json";
@@ -1260,6 +1262,22 @@ public class StructureChooser extends GStructureChooser
                   .associatePdbWithSeq(selectedPdbFileName,
                           DataSourceType.FILE, selectedSequence, true,
                           Desktop.instance);
+          /* LOOK AT
+          public PDBEntry associatePdbWithSeq(String choice, DataSourceType file,
+                  SequenceI sequence, boolean prompt,
+                  StructureSelectionManagerProvider ssmp)
+          IN AssociatePdbFileWithSeq */
+
+          // DO SOMETHING WITH
+          if (StructureChooser.this.localPdbPaeMatrixFileName != null)
+          {
+
+          }
+          if (StructureChooser.this.combo_tempFacAs
+                  .getSelectedItem() != null)
+          {
+
+          }
 
           sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry },
                   ap, new SequenceI[]
diff --git a/src/jalview/ws/dbsources/EBIAlfaFold.java b/src/jalview/ws/dbsources/EBIAlfaFold.java
index b3bcfd9..4ed28fc 100644
--- a/src/jalview/ws/dbsources/EBIAlfaFold.java
+++ b/src/jalview/ws/dbsources/EBIAlfaFold.java
@@ -292,14 +292,8 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
       if (ssm != null)
       {
         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");
 
         try
         {
@@ -368,24 +362,10 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
           String seqId) throws IOException, ParseException
   {
     SequenceI sequence = null;
-    /* debugging */
-    SequenceI[] seqs = pdbAlignment.getSequencesArray();
-    if (seqs == null)
-      Console.debug("******* sequences is null");
-    else
-    {
-      for (int i = 0; i < seqs.length; i++)
-      {
-        SequenceI s = seqs[i];
-      }
-    }
-    /* end debug */
     if (seqId == null)
     {
       int seqToGet = index > 0 ? index : 0;
       sequence = pdbAlignment.getSequenceAt(seqToGet);
-      Console.debug("***** Got sequence at index " + seqToGet + ": "
-              + (sequence == null ? null : sequence.getName()));
     }
     if (sequence == null)
     {
@@ -406,7 +386,6 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
     JSONObject paeDict = null;
     if (paeJson instanceof JSONObject)
     {
-      Console.debug("***** paeJson is a JSONObject");
       paeDict = (JSONObject) paeJson;
     }
     else if (paeJson instanceof JSONArray)
@@ -435,13 +414,10 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
           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;
-- 
1.7.10.2