JAL-3829 alternative UX: need to select 3d-beacons from dropdown if db-refs need...

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

diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index b349559..021e2f6 100644 (file)
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -65,6 +65,7 @@ import jalview.util.BrowserLauncher;
 import jalview.util.MessageManager;
 import jalview.ws.dbsources.EBIAlfaFold;
 import jalview.ws.dbsources.Pdb;
+import jalview.ws.utils.UrlDownloadClient;
 
 /**
  * Base class with common functionality for JMol, Chimera or other structure
@@ -154,6 +155,15 @@ public abstract class StructureViewerBase extends GStructureViewer
   {
     alignAddedStructures = alignAdded;
   }
+  
+  /**
+   * called by the binding model to indicate when adding structures is happening or has been completed
+   * @param addingStructures
+   */
+  public synchronized void setAddingStructures(boolean addingStructures)
+  {
+    this.addingStructures = addingStructures;
+  }
 
   /**
    * 
@@ -1077,7 +1087,7 @@ public abstract class StructureViewerBase extends GStructureViewer
     progressBar = pi;
   }
 
-  protected void setProgressMessage(String message, long id)
+  public void setProgressMessage(String message, long id)
   {
     if (progressBar != null)
     {
@@ -1144,7 +1154,25 @@ public abstract class StructureViewerBase extends GStructureViewer
       {
         pdbseq = afclient.getSequenceRecords(pdbid);
       } else {
-        pdbseq = pdbclient.getSequenceRecords(pdbid);
+          if (processingEntry.hasRetrievalUrl())
+          {
+            // retrieve from URL to new local tmpfile
+            File tmpFile = File.createTempFile(pdbid,
+                    "." + (PDBEntry.Type.MMCIF.toString().equals(
+                            processingEntry.getType().toString()) ? "cif"
+                                    : "pdb"));
+            String fromUrl = processingEntry.getRetrievalUrl();
+            UrlDownloadClient.download(fromUrl, tmpFile);
+            
+            // may not need this check ?
+            String file = tmpFile.getAbsolutePath();
+            if (file != null)
+            {
+              pdbseq = EBIAlfaFold.importDownloadedStructureFromUrl(fromUrl,tmpFile,pdbid,null,null,null);
+            }
+          } else {
+            pdbseq = pdbclient.getSequenceRecords(pdbid);
+          }
       }
     } catch (Exception e)
     {