JAL-629 Fix null AlignPanel. More descriptive label of pAE Matrix allows 'Add referen...

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

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 80024d9..3fce931 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -1266,9 +1266,9 @@ public class StructureChooser extends GStructureChooser
         }
         else if (currentView == VIEWS_FROM_FILE)
         {
-          TFType tft = (TFType) StructureChooser.this.combo_tempFacAs
-                  .getSelectedItem();
-          String paeFilename = StructureChooser.this.localPdbPaeMatrixFileName;
+          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();
@@ -1276,37 +1276,8 @@ public class StructureChooser extends GStructureChooser
             selectedSequence = userSelectedSeq;
           String pdbFilename = selectedPdbFileName;
 
-          PDBEntry fileEntry = new AssociatePdbFileWithSeq()
-                  .associatePdbWithSeq(pdbFilename, DataSourceType.FILE,
-                          selectedSequence, true, Desktop.instance, tft,
-                          paeFilename);
-
-          /*
-          SequenceI[] seqArray = new SequenceI[] { selectedSequence };
-          
-          StructureFile sf = ssm.computeMapping(true, seqArray, null,
-                  selectedPdbFileName, DataSourceType.FILE, null, tft,
-                  paeFilename);
-          StructureMapping[] sm = ssm.getMapping(fileEntry.getFile());
-          // DO SOMETHING WITH
-          File paeFile = paeFilename == null ? null : new File(paeFilename);
-          if (paeFilename != null && paeFile.exists())
-          {
-            AlignmentI al = StructureChooser.this.ap.getAlignment();
-            try
-            {
-              EBIAlfaFold.importPaeJSONAsContactMatrixToSequence(al,
-                      paeFile, selectedSequence);
-            } catch (IOException | ParseException e)
-            {
-              // TODO Auto-generated catch block
-              e.printStackTrace();
-            }
-          }
-          */
-          sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry },
-                  ap, new SequenceI[]
-                  { selectedSequence });
+          StructureChooser.openStructureFileForSequence(ssm, sc, ap,
+                  selectedSequence, true, pdbFilename, tft, paeFilename);
         }
         SwingUtilities.invokeLater(new Runnable()
         {
@@ -1735,30 +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();
   }
 }