Merge branch 'patch/JAL-2754_patch2104forJava8' into develop

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

diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index c8854a7..93d675a 100644 (file)
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -34,6 +34,7 @@ import jalview.io.JalviewFileView;
 import jalview.jbgui.GStructureViewer;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemes;
+import jalview.structure.StructureMapping;
 import jalview.structures.models.AAStructureBindingModel;
 import jalview.util.MessageManager;
 
@@ -102,9 +103,9 @@ public abstract class StructureViewerBase extends GStructureViewer
 
   protected boolean alignAddedStructures = false;
 
-  protected boolean _started = false;
+  protected volatile boolean _started = false;
 
-  protected boolean addingStructures = false;
+  protected volatile boolean addingStructures = false;
 
   protected Thread worker = null;
 
@@ -113,6 +114,13 @@ public abstract class StructureViewerBase extends GStructureViewer
   protected JMenu viewSelectionMenu;
 
   /**
+   * set after sequence colouring has been applied for this structure viewer.
+   * used to determine if the final sequence/structure mapping has been
+   * determined
+   */
+  protected volatile boolean seqColoursApplied = false;
+
+  /**
    * Default constructor
    */
   public StructureViewerBase()
@@ -310,6 +318,8 @@ public abstract class StructureViewerBase extends GStructureViewer
 
   public abstract ViewerType getViewerType();
 
+  protected abstract IProgressIndicator getIProgressIndicator();
+
   /**
    * add a new structure (with associated sequences and chains) to this viewer,
    * retrieving it if necessary first.
@@ -460,7 +470,7 @@ 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
@@ -907,6 +917,7 @@ public abstract class StructureViewerBase extends GStructureViewer
       {
         binding.colourBySequence(ap);
       }
+      seqColoursApplied = true;
     }
   }
 
@@ -1026,4 +1037,42 @@ public abstract class StructureViewerBase extends GStructureViewer
       seqColour_actionPerformed(null);
     }
   }
+
+  @Override
+  public boolean hasMapping()
+  {
+    if (worker != null && (addingStructures || _started))
+    {
+      return false;
+    }
+    if (getBinding() == null)
+    {
+      if (_aps == null || _aps.size() == 0)
+      {
+        // viewer has been closed, but we did at some point run.
+        return true;
+      }
+      return false;
+    }
+    String[] pdbids = getBinding().getStructureFiles();
+    if (pdbids == null)
+    {
+      return false;
+    }
+    int p=0;
+    for (String pdbid:pdbids) {
+      StructureMapping sm[] = getBinding().getSsm().getMapping(pdbid);
+      if (sm!=null && sm.length>0 && sm[0]!=null) {
+        p++;
+      }
+    }
+    // only return true if there is a mapping for every structure file we have loaded
+    if (p == 0 || p != pdbids.length)
+    {
+      return false;
+    }
+    // and that coloring has been applied
+    return seqColoursApplied;
+  }
+
 }