JAL-2465 bugfix and rerefactor renamed getPdbFile() method to getStructureFile()

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

diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index d7f7c31..6e7936b 100644 (file)
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -309,6 +309,10 @@ public abstract class StructureViewerBase extends GStructureViewer
 
   public abstract ViewerType getViewerType();
 
+  protected abstract AAStructureBindingModel getBindingModel();
+
+  protected abstract IProgressIndicator getIProgressIndicator();
+
   /**
    * add a new structure (with associated sequences and chains) to this viewer,
    * retrieving it if necessary first.
@@ -457,7 +461,7 @@ public abstract class StructureViewerBase extends GStructureViewer
      * create the mappings
      */
     apanel.getStructureSelectionManager().setMapping(seq, chains,
-            pdbFilename, DataSourceType.FILE);
+            pdbFilename, DataSourceType.FILE, getIProgressIndicator());
 
     /*
      * alert the FeatureRenderer to show new (PDB RESNUM) features
@@ -919,7 +923,7 @@ public abstract class StructureViewerBase extends GStructureViewer
       {
         // TODO: cope with multiple PDB files in view
         in = new BufferedReader(
-                new FileReader(getBinding().getPdbFile()[0]));
+                new FileReader(getBinding().getStructureFiles()[0]));
         File outFile = chooser.getSelectedFile();
   
         PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
@@ -991,7 +995,7 @@ public abstract class StructureViewerBase extends GStructureViewer
      * enable 'Superpose with' if more than one mapped structure
      */
     viewSelectionMenu.setEnabled(false);
-    if (getBinding().getPdbFile().length > 1
+    if (getBinding().getStructureFiles().length > 1
             && getBinding().getSequence().length > 1)
     {
       viewSelectionMenu.setEnabled(true);