Merge branch 'develop' into JAL-3416_different_look_and_feel_on_linux

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

diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index e180f6b..021e2f6 100644 (file)
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -61,8 +61,11 @@ import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemes;
 import jalview.structure.StructureMapping;
 import jalview.structures.models.AAStructureBindingModel;
+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
@@ -152,6 +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;
+  }
 
   /**
    * 
@@ -706,7 +718,7 @@ public abstract class StructureViewerBase extends GStructureViewer
                 }
                 else
                 {
-                  // update the Chimera display now.
+                  // update the viewer display now.
                   seqColour_actionPerformed();
                 }
               }
@@ -756,6 +768,10 @@ public abstract class StructureViewerBase extends GStructureViewer
       }
     });
 
+    viewerActionMenu.setText(getViewerName());
+    helpItem.setText(MessageManager.formatMessage("label.viewer_help",
+            getViewerName()));
+
     buildColourMenu();
   }
 
@@ -965,7 +981,7 @@ public abstract class StructureViewerBase extends GStructureViewer
      * enable 'Superpose with' if more than one mapped structure
      */
     viewSelectionMenu.setEnabled(false);
-    if (getBinding().getStructureFiles().length > 1
+    if (getBinding().getMappedStructureCount() > 1
             && getBinding().getSequence().length > 1)
     {
       viewSelectionMenu.setEnabled(true);
@@ -1071,7 +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)
     {
@@ -1116,6 +1132,7 @@ public abstract class StructureViewerBase extends GStructureViewer
   {
     String filePath = null;
     Pdb pdbclient = new Pdb();
+    EBIAlfaFold afclient =  new EBIAlfaFold();
     AlignmentI pdbseq = null;
     String pdbid = processingEntry.getId();
     long handle = System.currentTimeMillis()
@@ -1133,7 +1150,30 @@ public abstract class StructureViewerBase extends GStructureViewer
     // { pdbid }));
     try
     {
-      pdbseq = pdbclient.getSequenceRecords(pdbid);
+      if (afclient.isValidReference(pdbid))
+      {
+        pdbseq = afclient.getSequenceRecords(pdbid);
+      } else {
+          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)
     {
       System.err.println(
@@ -1204,6 +1244,9 @@ public abstract class StructureViewerBase extends GStructureViewer
         }
         forceClose = confirm == JvOptionPane.YES_OPTION;
       }
+    }
+    if (binding != null)
+    {
       binding.closeViewer(forceClose);
     }
     setAlignmentPanel(null);
@@ -1216,4 +1259,22 @@ public abstract class StructureViewerBase extends GStructureViewer
     dispose();
   }
 
+  @Override
+  public void showHelp_actionPerformed()
+  {
+    try
+    {
+      String url = getBinding().getHelpURL();
+      if (url != null)
+      {
+        BrowserLauncher.openURL(url);
+      }
+    } catch (IOException ex)
+    {
+      System.err
+              .println("Show " + getViewerName() + " failed with: "
+                      + ex.getMessage());
+    }
+  }
+
 }