JAL-2798 added != null check for Aptx trees

[jalview.git] / src / jalview / gui / Jalview2XML.java

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 4fffe6f..c0246c3 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -37,10 +37,15 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.StructureViewerModel;
 import jalview.datamodel.StructureViewerModel.StructureData;
+import jalview.ext.archaeopteryx.AptxInit;
+import jalview.ext.treeviewer.TreeFrameI;
+import jalview.ext.treeviewer.TreeI;
+import jalview.ext.treeviewer.TreeViewerUtils;
 import jalview.ext.varna.RnaModel;
 import jalview.gui.StructureViewer.ViewerType;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
+import jalview.io.NewickFile;
 import jalview.renderer.ResidueShaderI;
 import jalview.schemabinding.version2.AlcodMap;
 import jalview.schemabinding.version2.AlcodonFrame;
@@ -216,34 +221,6 @@ public class Jalview2XML
     }
   }
 
-  void clearSeqRefs()
-  {
-    if (_cleartables)
-    {
-      if (seqRefIds != null)
-      {
-        seqRefIds.clear();
-      }
-      if (seqsToIds != null)
-      {
-        seqsToIds.clear();
-      }
-      if (incompleteSeqs != null)
-      {
-        incompleteSeqs.clear();
-      }
-      // seqRefIds = null;
-      // seqsToIds = null;
-    }
-    else
-    {
-      // do nothing
-      warn("clearSeqRefs called when _cleartables was not set. Doing nothing.");
-      // seqRefIds = new Hashtable();
-      // seqsToIds = new IdentityHashMap();
-    }
-  }
-
   void initSeqRefs()
   {
     if (seqsToIds == null)
@@ -1123,9 +1100,35 @@ public class Jalview2XML
               jms.addTree(tree);
             }
           }
+
         }
       }
     }
+    if (!storeDS && av.getCurrentExtTree() != null)
+    {
+      Set<TreeFrameI> externalTreeViews = TreeViewerUtils
+              .getActiveTreeViews()
+              .keySet();
+      for (TreeFrameI treeView : externalTreeViews)
+      {
+        TreeI tree = treeView.getTree();
+        try
+        {
+          tree.writeToXml(new File("word"));
+          copyFileToJar(jout, "word", "aptx-test");
+
+
+        } catch (IOException e)
+        {
+          // TODO Auto-generated catch block
+          e.printStackTrace();
+        }
+
+      }
+
+    }
+
+
 
     // SAVE ANNOTATIONS
     /**
@@ -1554,7 +1557,7 @@ public class Jalview2XML
 
                 String varnaStateFile = varna.getStateInfo(model.rna);
                 jarEntryName = RNA_PREFIX + viewId + "_" + nextCounter();
-                copyFileToJar(jout, varnaStateFile, jarEntryName);
+
                 rnaSessions.put(model, jarEntryName);
               }
               SecondaryStructure ss = new SecondaryStructure();
@@ -2295,6 +2298,7 @@ public class Jalview2XML
 
       jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
       af = loadJalviewAlign(jprovider);
+      af.setMenusForViewport();
 
     } catch (MalformedURLException e)
     {
@@ -3559,12 +3563,33 @@ public class Jalview2XML
     if (loadTreesAndStructures)
     {
       loadTrees(jms, view, af, av, ap);
+      loadExternalTrees(jprovider, jms, av);
       loadPDBStructures(jprovider, jseqs, af, ap);
       loadRnaViewers(jprovider, jseqs, ap);
     }
     // and finally return.
     return af;
   }
+    
+  private void loadExternalTrees(jarInputStreamProvider jprovider,
+          JalviewModelSequence jms, AlignViewport av)
+  {
+    String treeFile = copyJarEntry(jprovider, "aptx-test", "aptx", null);
+    if (treeFile != null)
+    {
+    try
+    {
+      AptxInit.createInstancesFromFile(treeFile, av);
+    } catch (IOException e)
+    {
+      // TODO Auto-generated catch block
+      e.printStackTrace();
+      }
+    }
+    
+  }
+
+
 
   /**
    * Instantiate and link any saved RNA (Varna) viewers. The state of the Varna
@@ -3680,12 +3705,20 @@ public class Jalview2XML
       {
 
         Tree tree = jms.getTree(t);
+        NewickFile newick = new jalview.io.NewickFile(tree.getNewick());
+
+        TreeFrameI externalViewer = AptxInit.createInstanceFromNhx(
+                tree.getTitle(), tree.getNewick(),
+                av);
+
 
         TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
         if (tp == null)
         {
+
+
           tp = af.showNewickTree(
-                  new jalview.io.NewickFile(tree.getNewick()),
+                  newick,
                   tree.getTitle(), tree.getWidth(), tree.getHeight(),
                   tree.getXpos(), tree.getYpos());
           if (tree.getId() != null)
@@ -4249,7 +4282,8 @@ public class Jalview2XML
       StructureData filedat = oldFiles.get(id);
       String pdbFile = filedat.getFilePath();
       SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]);
-      binding.getSsm().setMapping(seq, null, pdbFile, DataSourceType.FILE);
+      binding.getSsm().setMapping(seq, null, pdbFile, DataSourceType.FILE,
+              null);
       binding.addSequenceForStructFile(pdbFile, seq);
     }
     // and add the AlignmentPanel's reference to the view panel
@@ -5341,28 +5375,25 @@ public class Jalview2XML
 
   }
 
-  public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap,
-          boolean keepSeqRefs)
+  /**
+   * Provides a 'copy' of an alignment view (on action New View) by 'saving' the
+   * view as XML (but not to file), and then reloading it
+   * 
+   * @param ap
+   * @return
+   */
+  public AlignmentPanel copyAlignPanel(AlignmentPanel ap)
   {
     initSeqRefs();
     JalviewModel jm = saveState(ap, null, null, null);
 
-    if (!keepSeqRefs)
-    {
-      clearSeqRefs();
-      jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
-    }
-    else
-    {
-      uniqueSetSuffix = "";
-      jm.getJalviewModelSequence().getViewport(0).setId(null); // we don't
-      // overwrite the
-      // view we just
-      // copied
-    }
+    uniqueSetSuffix = "";
+    jm.getJalviewModelSequence().getViewport(0).setId(null);
+    // we don't overwrite the view we just copied
+
     if (this.frefedSequence == null)
     {
-      frefedSequence = new Vector();
+      frefedSequence = new Vector<>();
     }
 
     viewportsAdded.clear();
@@ -5382,32 +5413,8 @@ public class Jalview2XML
     return af.alignPanel;
   }
 
-  /**
-   * flag indicating if hashtables should be cleared on finalization TODO this
-   * flag may not be necessary
-   */
-  private final boolean _cleartables = true;
-
   private Hashtable jvids2vobj;
 
-  /*
-   * (non-Javadoc)
-   * 
-   * @see java.lang.Object#finalize()
-   */
-  @Override
-  protected void finalize() throws Throwable
-  {
-    // really make sure we have no buried refs left.
-    if (_cleartables)
-    {
-      clearSeqRefs();
-    }
-    this.seqRefIds = null;
-    this.seqsToIds = null;
-    super.finalize();
-  }
-
   private void warn(String msg)
   {
     warn(msg, null);