JAL-629 stash some TFType and PAEFile info into a PDBEntry

[jalview.git] / src / jalview / gui / StructureChooser.java

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 47bec31..3fce931 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -43,12 +43,15 @@ import javax.swing.JTable;
 import javax.swing.SwingUtilities;
 import javax.swing.table.AbstractTableModel;
 
+import com.stevesoft.pat.Regex;
+
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
 import jalview.bin.Console;
 import jalview.bin.Jalview;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.ext.jmol.JmolParser;
 import jalview.fts.api.FTSData;
 import jalview.fts.api.FTSDataColumnI;
 import jalview.fts.api.FTSRestClientI;
@@ -679,7 +682,18 @@ public class StructureChooser extends GStructureChooser
     {
       selectedPdbFileName = chooser.getSelectedFile().getPath();
       Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
+      boolean guessTFType = localPdbPaeMatrixFileName == null;
       localPdbPaeMatrixFileName = guessPAEFilename();
+      guessTFType |= localPdbPaeMatrixFileName != null;
+      Regex alphaFold = JmolParser.getNewAlphafoldValidator();
+      if (guessTFType
+              && alphaFold.search(new File(selectedPdbFileName).getName())
+              && !tempFacAsChanged)
+      {
+        // localPdbPaeMatrixFileName was null and now isn't and filename could
+        // well be AlphaFold and user hasn't adjusted the tempFacType
+        combo_tempFacAs.setSelectedItem(TFType.PLDDT);
+      }
       validateSelections();
     }
   }
@@ -725,7 +739,9 @@ 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";
@@ -1250,20 +1266,18 @@ public class StructureChooser extends GStructureChooser
         }
         else if (currentView == VIEWS_FROM_FILE)
         {
-          SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
-                  .getCmb_assSeq().getSelectedItem()).getSequence();
+          StructureChooser sc = StructureChooser.this;
+          TFType tft = (TFType) sc.combo_tempFacAs.getSelectedItem();
+          String paeFilename = sc.localPdbPaeMatrixFileName;
+          AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel
+                  .getCmb_assSeq().getSelectedItem();
+          SequenceI userSelectedSeq = assSeqOpt.getSequence();
           if (userSelectedSeq != null)
-          {
             selectedSequence = userSelectedSeq;
-          }
-          PDBEntry fileEntry = new AssociatePdbFileWithSeq()
-                  .associatePdbWithSeq(selectedPdbFileName,
-                          DataSourceType.FILE, selectedSequence, true,
-                          Desktop.instance);
+          String pdbFilename = selectedPdbFileName;
 
-          sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry },
-                  ap, new SequenceI[]
-                  { selectedSequence });
+          StructureChooser.openStructureFileForSequence(ssm, sc, ap,
+                  selectedSequence, true, pdbFilename, tft, paeFilename);
         }
         SwingUtilities.invokeLater(new Runnable()
         {
@@ -1393,6 +1407,7 @@ public class StructureChooser extends GStructureChooser
       setProgressBar(MessageManager.formatMessage(
               "status.fetching_3d_structures_for",
               pdbEntriesToView[0].getId()), progressId);
+      // Can we pass a pre-computeMappinged pdbFile?
       theViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
     }
     setProgressBar(null, progressId);
@@ -1691,30 +1706,29 @@ public class StructureChooser extends GStructureChooser
   /**
    * Open a single structure file for a given sequence
    */
-  public static void openStructureFileForSequence(AlignmentPanel ap,
-          SequenceI seq, File sFile)
+  public static void openStructureFileForSequence(
+          StructureSelectionManager ssm, StructureChooser sc,
+          AlignmentPanel ap, SequenceI seq, boolean prompt,
+          String sFilename, TFType tft, String paeFilename)
   {
-    // Open the chooser headlessly. Not sure this is actually needed ?
-    StructureChooser sc = new StructureChooser(new SequenceI[] { seq }, seq,
-            ap, false);
-    StructureSelectionManager ssm = ap.getStructureSelectionManager();
-    PDBEntry fileEntry = null;
-    try
-    {
-      fileEntry = new AssociatePdbFileWithSeq().associatePdbWithSeq(
-              sFile.getAbsolutePath(), DataSourceType.FILE, seq, true,
-              Desktop.instance);
-    } catch (Exception e)
-    {
-      Console.error("Could not open structure file '"
-              + sFile.getAbsolutePath() + "'");
-      return;
+    boolean headless = false;
+    if (sc == null)
+    {
+      headless = true;
+      sc = new StructureChooser(new SequenceI[] { seq }, seq, ap, false);
     }
+    if (ssm == null)
+      ssm = ap.getStructureSelectionManager();
+
+    PDBEntry fileEntry = new AssociatePdbFileWithSeq().associatePdbWithSeq(
+            sFilename, DataSourceType.FILE, seq, prompt, Desktop.instance,
+            tft, paeFilename);
 
     StructureViewer sViewer = sc.launchStructureViewer(ssm,
             new PDBEntry[]
             { fileEntry }, ap, new SequenceI[] { seq });
 
-    sc.mainFrame.dispose();
+    if (headless)
+      sc.mainFrame.dispose();
   }
 }