X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureViewerBase.java;h=93d675acf785acc05db92a3b8f9578316cdfccc4;hb=33f8761fdb05b594fd8a3341180256003d3a91df;hp=3ba9947e5e2477fbbbf1a1f8220b5d34867bb880;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git

diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index 3ba9947..93d675a 100644
--- 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;
 
@@ -83,18 +84,18 @@ public abstract class StructureViewerBase extends GStructureViewer
   /**
    * list of sequenceSet ids associated with the view
    */
-  protected List<String> _aps = new ArrayList<String>();
+  protected List<String> _aps = new ArrayList<>();
 
   /**
    * list of alignment panels to use for superposition
    */
-  protected Vector<AlignmentPanel> _alignwith = new Vector<AlignmentPanel>();
+  protected Vector<AlignmentPanel> _alignwith = new Vector<>();
 
   /**
    * list of alignment panels that are used for colouring structures by aligned
    * sequences
    */
-  protected Vector<AlignmentPanel> _colourwith = new Vector<AlignmentPanel>();
+  protected Vector<AlignmentPanel> _colourwith = new Vector<>();
 
   private String viewId = null;
 
@@ -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()
@@ -170,7 +178,7 @@ public abstract class StructureViewerBase extends GStructureViewer
   {
     if (_alignwith == null)
     {
-      _alignwith = new Vector<AlignmentPanel>();
+      _alignwith = new Vector<>();
     }
     if (_alignwith.size() == 0 && ap != null)
     {
@@ -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
@@ -468,7 +478,9 @@ public abstract class StructureViewerBase extends GStructureViewer
     if (apanel.getSeqPanel().seqCanvas.fr != null)
     {
       apanel.getSeqPanel().seqCanvas.fr.featuresAdded();
-      apanel.paintAlignment(true);
+      // note - we don't do a refresh for structure here because we do it
+      // explicitly for all panels later on
+      apanel.paintAlignment(true, false);
     }
 
     /*
@@ -717,11 +729,11 @@ public abstract class StructureViewerBase extends GStructureViewer
 
     if (_colourwith == null)
     {
-      _colourwith = new Vector<AlignmentPanel>();
+      _colourwith = new Vector<>();
     }
     if (_alignwith == null)
     {
-      _alignwith = new Vector<AlignmentPanel>();
+      _alignwith = new Vector<>();
     }
 
     ViewSelectionMenu seqColourBy = new ViewSelectionMenu(
@@ -888,7 +900,7 @@ public abstract class StructureViewerBase extends GStructureViewer
     binding.setColourBySequence(seqColour.isSelected());
     if (_colourwith == null)
     {
-      _colourwith = new Vector<AlignmentPanel>();
+      _colourwith = new Vector<>();
     }
     if (binding.isColourBySequence())
     {
@@ -905,6 +917,7 @@ public abstract class StructureViewerBase extends GStructureViewer
       {
         binding.colourBySequence(ap);
       }
+      seqColoursApplied = true;
     }
   }
 
@@ -1024,4 +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;
+  }
+
 }