Merge branch 'codereviews/JAL-1990_IProgressIndicator_jalview.structure' into patch...

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

diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index ba360af..89de2e8 100644 (file)
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -358,7 +358,7 @@ public class ChimeraViewFrame extends StructureViewerBase
   @Override
   protected List<StructureViewerBase> getViewersFor(AlignmentPanel ap)
   {
-    List<StructureViewerBase> result = new ArrayList<StructureViewerBase>();
+    List<StructureViewerBase> result = new ArrayList<>();
     JInternalFrame[] frames = Desktop.instance.getAllFrames();
 
     for (JInternalFrame frame : frames)
@@ -414,7 +414,7 @@ public class ChimeraViewFrame extends StructureViewerBase
   @Override
   void showSelectedChains()
   {
-    List<String> toshow = new ArrayList<String>();
+    List<String> toshow = new ArrayList<>();
     for (int i = 0; i < chainMenu.getItemCount(); i++)
     {
       if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
@@ -484,8 +484,8 @@ public class ChimeraViewFrame extends StructureViewerBase
     // todo - record which pdbids were successfully imported.
     StringBuilder errormsgs = new StringBuilder(128);
     StringBuilder files = new StringBuilder(128);
-    List<PDBEntry> filePDB = new ArrayList<PDBEntry>();
-    List<Integer> filePDBpos = new ArrayList<Integer>();
+    List<PDBEntry> filePDB = new ArrayList<>();
+    List<Integer> filePDBpos = new ArrayList<>();
     PDBEntry thePdbEntry = null;
     StructureFile pdb = null;
     try
@@ -598,9 +598,12 @@ public class ChimeraViewFrame extends StructureViewerBase
               stopProgressBar("", startTime);
             }
             // Explicitly map to the filename used by Chimera ;
+
             pdb = jmb.getSsm().setMapping(jmb.getSequence()[pos],
-                    jmb.getChains()[pos], pe.getFile(), protocol);
+                    jmb.getChains()[pos], pe.getFile(), protocol,
+                    progressBar);
             stashFoundChains(pdb, pe.getFile());
+
           } catch (OutOfMemoryError oomerror)
           {
             new OOMWarning(
@@ -658,7 +661,7 @@ public class ChimeraViewFrame extends StructureViewerBase
 
   /**
    * Fetch PDB data and save to a local file. Returns the full path to the file,
-   * or null if fetch fails.
+   * or null if fetch fails. TODO: refactor to common with Jmol ? duplication
    * 
    * @param processingEntry
    * @return
@@ -891,4 +894,10 @@ public class ChimeraViewFrame extends StructureViewerBase
     }
     return reply;
   }
+
+  @Override
+  protected IProgressIndicator getIProgressIndicator()
+  {
+    return progressBar;
+  }
 }