JAL-629 removed debug prints. added .cif. added some comments/code-markers

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

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 47bec31..11e50db 100644 (file)
--- 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[]