From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 30 May 2017 09:33:32 +0000 (+0100)
Subject: Merge branch 'develop' into features/JAL-2446NCList
X-Git-Tag: Release_2_10_3b1~224
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=b94e9d2b3e667c6925e3e40bac63de219fc717a7;hp=c63940e40edf030d8bb76d41fbd6b56331046427;p=jalview.git

Merge branch 'develop' into features/JAL-2446NCList

Conflicts:
	src/jalview/appletgui/SeqPanel.java
---

diff --git a/help/html/releases.html b/help/html/releases.html
index cc6e96c..18f8f43 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -85,6 +85,11 @@ li:before {
               <!-- JAL-2535 -->Posterior probability annotation from
               Stockholm files imported as sequence associated annotation
             </li>
+            <li>
+              <!-- JAL-2533 -->Sequence names don't include file
+              extension when importing structure files without embedded
+              names or PDB accessions
+            </li>
           </ul>
           <em>Application</em>
           <ul>
@@ -169,7 +174,12 @@ li:before {
           <li><!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get shown again after pressing 'Cancel'</li>
           <li><!--  JAL-2461 -->DAS registry not found exceptions removed from console output</li>
           <li><!--  JAL-2383 -->Above PID colour threshold not recovered when alignment view imported from project</li> 
-          
+          <li><!-- JAL-2465 -->No mappings generated between structure and sequences extracted from structure files imported via URL</li>
+            <li>
+              <!-- JAL-2520 -->Structures loaded via URL are saved in
+              Jalview Projects rather than fetched via URL again when
+              the project is loaded and the structure viewed
+            </li>
           </ul>
           <em>Applet</em>
           <ul>
diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java
index c454203..39111c3 100644
--- a/src/MCview/AppletPDBCanvas.java
+++ b/src/MCview/AppletPDBCanvas.java
@@ -1119,7 +1119,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
   // ////////////////////////////////
   // /StructureListener
   @Override
-  public String[] getPdbFile()
+  public String[] getStructureFiles()
   {
     return new String[] { pdbentry.getFile() };
   }
diff --git a/src/MCview/PDBCanvas.java b/src/MCview/PDBCanvas.java
index ff1211a..83642cc 100644
--- a/src/MCview/PDBCanvas.java
+++ b/src/MCview/PDBCanvas.java
@@ -1075,7 +1075,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
   // ////////////////////////////////
   // /StructureListener
   @Override
-  public String[] getPdbFile()
+  public String[] getStructureFiles()
   {
     return new String[] { pdbentry.getFile() };
   }
diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 1ca4256..ab6dd9a 100644
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -586,13 +586,13 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   @Override
   public void mouseReleased(MouseEvent evt)
   {
+    boolean didDrag = mouseDragging; // did we come here after a drag
     mouseDragging = false;
     mouseWheelPressed = false;
-    ap.paintAlignment(true);
 
     if (!editingSeqs)
     {
-      doMouseReleasedDefineMode(evt);
+      doMouseReleasedDefineMode(evt, didDrag);
       return;
     }
 
@@ -1485,7 +1485,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
   }
 
-  public void doMouseReleasedDefineMode(MouseEvent evt)
+  public void doMouseReleasedDefineMode(MouseEvent evt, boolean afterDrag)
   {
     if (stretchGroup == null)
     {
@@ -1495,7 +1495,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     // but defer colourscheme update until hidden sequences are passed in
     boolean vischange = stretchGroup.recalcConservation(true);
     // here we rely on stretchGroup == av.getSelection()
-    needOverviewUpdate |= vischange && av.isSelectionDefinedGroup();
+    needOverviewUpdate |= vischange && av.isSelectionDefinedGroup()
+            && afterDrag;
     if (stretchGroup.cs != null)
     {
       stretchGroup.cs.alignmentChanged(stretchGroup,
diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index fcb6109..5d91b36 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -73,7 +73,7 @@ public class Alignment implements AlignmentI
     groups = Collections.synchronizedList(new ArrayList<SequenceGroup>());
     hiddenSequences = new HiddenSequences(this);
     hiddenCols = new HiddenColumns();
-    codonFrameList = new ArrayList<AlignedCodonFrame>();
+    codonFrameList = new ArrayList<>();
 
     nucleotide = Comparison.isNucleotide(seqs);
 
@@ -405,7 +405,7 @@ public class Alignment implements AlignmentI
   @Override
   public SequenceGroup[] findAllGroups(SequenceI s)
   {
-    ArrayList<SequenceGroup> temp = new ArrayList<SequenceGroup>();
+    ArrayList<SequenceGroup> temp = new ArrayList<>();
 
     synchronized (groups)
     {
@@ -456,7 +456,7 @@ public class Alignment implements AlignmentI
             return;
           }
         }
-        sg.setContext(this);
+        sg.setContext(this, true);
         groups.add(sg);
       }
     }
@@ -533,7 +533,7 @@ public class Alignment implements AlignmentI
       }
       for (SequenceGroup sg : groups)
       {
-        sg.setContext(null);
+        sg.setContext(null, false);
       }
       groups.clear();
     }
@@ -549,7 +549,7 @@ public class Alignment implements AlignmentI
       {
         removeAnnotationForGroup(g);
         groups.remove(g);
-        g.setContext(null);
+        g.setContext(null, false);
       }
     }
   }
@@ -1071,7 +1071,7 @@ public class Alignment implements AlignmentI
     {
       return;
     }
-    List<SequenceI> toProcess = new ArrayList<SequenceI>();
+    List<SequenceI> toProcess = new ArrayList<>();
     toProcess.add(currentSeq);
     while (toProcess.size() > 0)
     {
@@ -1124,7 +1124,7 @@ public class Alignment implements AlignmentI
       return;
     }
     // try to avoid using SequenceI.equals at this stage, it will be expensive
-    Set<SequenceI> seqs = new LinkedIdentityHashSet<SequenceI>();
+    Set<SequenceI> seqs = new LinkedIdentityHashSet<>();
 
     for (int i = 0; i < getHeight(); i++)
     {
@@ -1409,7 +1409,7 @@ public class Alignment implements AlignmentI
     {
       return null;
     }
-    List<AlignedCodonFrame> cframes = new ArrayList<AlignedCodonFrame>();
+    List<AlignedCodonFrame> cframes = new ArrayList<>();
     for (AlignedCodonFrame acf : getCodonFrames())
     {
       if (acf.involvesSequence(seq))
@@ -1486,7 +1486,7 @@ public class Alignment implements AlignmentI
     if (sqs != null)
     {
       // avoid self append deadlock by
-      List<SequenceI> toappendsq = new ArrayList<SequenceI>();
+      List<SequenceI> toappendsq = new ArrayList<>();
       synchronized (sqs)
       {
         for (SequenceI addedsq : sqs)
@@ -1627,7 +1627,7 @@ public class Alignment implements AlignmentI
   @Override
   public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
   {
-    List<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+    List<AlignmentAnnotation> aa = new ArrayList<>();
     AlignmentAnnotation[] alignmentAnnotation = getAlignmentAnnotation();
     if (alignmentAnnotation != null)
     {
@@ -1648,7 +1648,7 @@ public class Alignment implements AlignmentI
   public Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
           String calcId, String label)
   {
-    ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+    ArrayList<AlignmentAnnotation> aa = new ArrayList<>();
     for (AlignmentAnnotation ann : getAlignmentAnnotation())
     {
       if ((calcId == null || (ann.getCalcId() != null && ann.getCalcId()
@@ -1853,7 +1853,7 @@ public class Alignment implements AlignmentI
   @Override
   public Set<String> getSequenceNames()
   {
-    Set<String> names = new HashSet<String>();
+    Set<String> names = new HashSet<>();
     for (SequenceI seq : getSequences())
     {
       names.add(seq.getName());
diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 76ad093..463b909 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -52,6 +52,12 @@ public class SequenceGroup implements AnnotatedCollectionI
   boolean colourText = false;
 
   /**
+   * True if the group is defined as a group on the alignment, false if it is
+   * just a selection.
+   */
+  boolean isDefined = false;
+
+  /**
    * after Olivier's non-conserved only character display
    */
   boolean showNonconserved = false;
@@ -59,7 +65,7 @@ public class SequenceGroup implements AnnotatedCollectionI
   /**
    * group members
    */
-  private List<SequenceI> sequences = new ArrayList<SequenceI>();
+  private List<SequenceI> sequences = new ArrayList<>();
 
   /**
    * representative sequence for this group (if any)
@@ -104,13 +110,23 @@ public class SequenceGroup implements AnnotatedCollectionI
    */
   private boolean normaliseSequenceLogo;
 
-  /**
-   * @return the includeAllConsSymbols
+  /*
+   * visibility of rows or represented rows covered by group
    */
-  public boolean isShowSequenceLogo()
-  {
-    return showSequenceLogo;
-  }
+  private boolean hidereps = false;
+
+  /*
+   * visibility of columns intersecting this group
+   */
+  private boolean hidecols = false;
+
+  AlignmentAnnotation consensus = null;
+
+  AlignmentAnnotation conservation = null;
+
+  private boolean showConsensusHistogram;
+
+  private AnnotatedCollectionI context;
 
   /**
    * Creates a new SequenceGroup object.
@@ -161,7 +177,7 @@ public class SequenceGroup implements AnnotatedCollectionI
     this();
     if (seqsel != null)
     {
-      sequences = new ArrayList<SequenceI>();
+      sequences = new ArrayList<>();
       sequences.addAll(seqsel.sequences);
       if (seqsel.groupName != null)
       {
@@ -172,13 +188,17 @@ public class SequenceGroup implements AnnotatedCollectionI
       colourText = seqsel.colourText;
       startRes = seqsel.startRes;
       endRes = seqsel.endRes;
-      cs = seqsel.cs;
+      cs = new ResidueShader(seqsel.getColourScheme());
       if (seqsel.description != null)
       {
         description = new String(seqsel.description);
       }
       hidecols = seqsel.hidecols;
       hidereps = seqsel.hidereps;
+      showNonconserved = seqsel.showNonconserved;
+      showSequenceLogo = seqsel.showSequenceLogo;
+      normaliseSequenceLogo = seqsel.normaliseSequenceLogo;
+      showConsensusHistogram = seqsel.showConsensusHistogram;
       idColour = seqsel.idColour;
       outlineColour = seqsel.outlineColour;
       seqrep = seqsel.seqrep;
@@ -195,6 +215,11 @@ public class SequenceGroup implements AnnotatedCollectionI
     }
   }
 
+  public boolean isShowSequenceLogo()
+  {
+    return showSequenceLogo;
+  }
+
   public SequenceI[] getSelectionAsNewSequences(AlignmentI align)
   {
     int iSize = sequences.size();
@@ -311,7 +336,7 @@ public class SequenceGroup implements AnnotatedCollectionI
     }
     else
     {
-      List<SequenceI> allSequences = new ArrayList<SequenceI>();
+      List<SequenceI> allSequences = new ArrayList<>();
       for (SequenceI seq : sequences)
       {
         allSequences.add(seq);
@@ -951,11 +976,6 @@ public class SequenceGroup implements AnnotatedCollectionI
   }
 
   /**
-   * visibility of rows or represented rows covered by group
-   */
-  private boolean hidereps = false;
-
-  /**
    * set visibility of sequences covered by (if no sequence representative is
    * defined) or represented by this group.
    * 
@@ -977,11 +997,6 @@ public class SequenceGroup implements AnnotatedCollectionI
   }
 
   /**
-   * visibility of columns intersecting this group
-   */
-  private boolean hidecols = false;
-
-  /**
    * set intended visibility of columns covered by this group
    * 
    * @param visibility
@@ -1015,7 +1030,7 @@ public class SequenceGroup implements AnnotatedCollectionI
   {
     SequenceGroup sgroup = new SequenceGroup(this);
     SequenceI[] insect = getSequencesInOrder(alignment);
-    sgroup.sequences = new ArrayList<SequenceI>();
+    sgroup.sequences = new ArrayList<>();
     for (int s = 0; insect != null && s < insect.length; s++)
     {
       if (map == null || map.containsKey(insect[s]))
@@ -1043,13 +1058,6 @@ public class SequenceGroup implements AnnotatedCollectionI
     this.showNonconserved = displayNonconserved;
   }
 
-  AlignmentAnnotation consensus = null, conservation = null;
-
-  /**
-   * flag indicating if consensus histogram should be rendered
-   */
-  private boolean showConsensusHistogram;
-
   /**
    * set this alignmentAnnotation object as the one used to render consensus
    * annotation
@@ -1242,7 +1250,7 @@ public class SequenceGroup implements AnnotatedCollectionI
   {
     // TODO add in other methods like 'getAlignmentAnnotation(String label),
     // etc'
-    ArrayList<AlignmentAnnotation> annot = new ArrayList<AlignmentAnnotation>();
+    ArrayList<AlignmentAnnotation> annot = new ArrayList<>();
     synchronized (sequences)
     {
       for (SequenceI seq : sequences)
@@ -1274,7 +1282,7 @@ public class SequenceGroup implements AnnotatedCollectionI
   @Override
   public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
   {
-    List<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+    List<AlignmentAnnotation> aa = new ArrayList<>();
     if (calcId == null)
     {
       return aa;
@@ -1293,7 +1301,7 @@ public class SequenceGroup implements AnnotatedCollectionI
   public Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
           String calcId, String label)
   {
-    ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+    ArrayList<AlignmentAnnotation> aa = new ArrayList<>();
     for (AlignmentAnnotation ann : getAlignmentAnnotation())
     {
       if ((calcId == null || (ann.getCalcId() != null && ann.getCalcId()
@@ -1340,12 +1348,29 @@ public class SequenceGroup implements AnnotatedCollectionI
     }
   }
 
-  private AnnotatedCollectionI context;
+  /**
+   * Sets the alignment or group context for this group, and whether it is
+   * defined as a group
+   * 
+   * @param ctx
+   *          the context for the group
+   * @param defined
+   *          whether the group is defined on the alignment or is just a
+   *          selection
+   * @throws IllegalArgumentException
+   *           if setting the context would result in a circular reference chain
+   */
+  public void setContext(AnnotatedCollectionI ctx, boolean defined)
+  {
+    setContext(ctx);
+    this.isDefined = defined;
+  }
 
   /**
    * Sets the alignment or group context for this group
    * 
    * @param ctx
+   *          the context for the group
    * @throws IllegalArgumentException
    *           if setting the context would result in a circular reference chain
    */
@@ -1375,6 +1400,11 @@ public class SequenceGroup implements AnnotatedCollectionI
     return context;
   }
 
+  public boolean isDefined()
+  {
+    return isDefined;
+  }
+
   public void setColourScheme(ColourSchemeI scheme)
   {
     if (cs == null)
diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 00fd679..5de554b 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -164,7 +164,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   public void closeViewer()
   {
     // remove listeners for all structures in viewer
-    getSsm().removeStructureViewerListener(this, this.getPdbFile());
+    getSsm().removeStructureViewerListener(this, this.getStructureFiles());
     viewer.dispose();
     lastCommand = null;
     viewer = null;
@@ -250,7 +250,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
      * get the distinct structure files modelled
      * (a file with multiple chains may map to multiple sequences)
      */
-    String[] files = getPdbFile();
+    String[] files = getStructureFiles();
     if (!waitForFileLoad(files))
     {
       return null;
@@ -577,7 +577,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
   private int getModelNum(String modelFileName)
   {
-    String[] mfn = getPdbFile();
+    String[] mfn = getStructureFiles();
     if (mfn == null)
     {
       return -1;
@@ -601,8 +601,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
   // ////////////////////////////////
   // /StructureListener
-  @Override
-  public synchronized String[] getPdbFile()
+  // @Override
+  public synchronized String[] getPdbFilex()
   {
     if (viewer == null)
     {
@@ -667,6 +667,32 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     return modelFileNames;
   }
 
+  @Override
+  public synchronized String[] getStructureFiles()
+  {
+    List<String> mset = new ArrayList<String>();
+    if (viewer == null)
+    {
+      return new String[0];
+    }
+
+    if (modelFileNames == null)
+    {
+      int modelCount = viewer.ms.mc;
+      String filePath = null;
+      for (int i = 0; i < modelCount; ++i)
+      {
+        filePath = viewer.ms.getModelFileName(i);
+        if (!mset.contains(filePath))
+        {
+          mset.add(filePath);
+        }
+      }
+      modelFileNames = mset.toArray(new String[mset.size()]);
+    }
+
+    return modelFileNames;
+  }
   /**
    * map from string to applet
    */
@@ -1035,7 +1061,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     chainNames = new ArrayList<String>();
     chainFile = new Hashtable<String, String>();
     boolean notifyLoaded = false;
-    String[] modelfilenames = getPdbFile();
+    String[] modelfilenames = getStructureFiles();
     // first check if we've lost any structures
     if (oldmodels != null && oldmodels.length > 0)
     {
diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
index 870c4fe..b954677 100644
--- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@ -289,7 +289,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    */
   public void closeViewer(boolean closeChimera)
   {
-    getSsm().removeStructureViewerListener(this, this.getPdbFile());
+    getSsm().removeStructureViewerListener(this, this.getStructureFiles());
     if (closeChimera)
     {
       viewer.exitChimera();
@@ -340,7 +340,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
           int[] _refStructure, HiddenColumns[] _hiddenCols)
   {
     StringBuilder allComs = new StringBuilder(128);
-    String[] files = getPdbFile();
+    String[] files = getStructureFiles();
 
     if (!waitForFileLoad(files))
     {
@@ -577,7 +577,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
      * to the Chimera command 'list models type molecule', see
      * ChimeraManager.getModelList().
      */
-    List<ChimeraModel> maps = chimeraMaps.get(getPdbFile()[pdbfnum]);
+    List<ChimeraModel> maps = chimeraMaps.get(getStructureFiles()[pdbfnum]);
     boolean hasSubModels = maps != null && maps.size() > 1;
     return "#" + String.valueOf(pdbfnum) + (hasSubModels ? ".1" : "");
   }
@@ -745,7 +745,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   // ////////////////////////////////
   // /StructureListener
   @Override
-  public synchronized String[] getPdbFile()
+  public synchronized String[] getStructureFiles()
   {
     if (viewer == null)
     {
@@ -1100,7 +1100,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     // TODO refactor as required to pull up to an interface
     AlignmentI alignment = avp.getAlignment();
 
-    String[] files = getPdbFile();
+    String[] files = getStructureFiles();
     if (files == null)
     {
       return 0;
diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 5d23f49..68a847e 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -410,8 +410,8 @@ public class AppJmol extends StructureViewerBase
     int waitFor = 35;
     int waitTotal = 0;
     while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()
-            : !(jmb.isFinishedInit() && jmb.getPdbFile() != null && jmb
-                    .getPdbFile().length == files.size()))
+            : !(jmb.isFinishedInit() && jmb.getStructureFiles() != null && jmb
+                    .getStructureFiles().length == files.size()))
     {
       try
       {
@@ -429,7 +429,7 @@ public class AppJmol extends StructureViewerBase
 //        System.err.println("finished: " + jmb.isFinishedInit()
 //                + "; loaded: " + Arrays.toString(jmb.getPdbFile())
 //                + "; files: " + files.toString());
-        jmb.getPdbFile();
+        jmb.getStructureFiles();
         break;
       }
     }
@@ -494,7 +494,7 @@ public class AppJmol extends StructureViewerBase
     String pdbid = "";
     try
     {
-      String[] filesInViewer = jmb.getPdbFile();
+      String[] filesInViewer = jmb.getStructureFiles();
       // TODO: replace with reference fetching/transfer code (validate PDBentry
       // as a DBRef?)
       Pdb pdbclient = new Pdb();
diff --git a/src/jalview/gui/AppVarnaBinding.java b/src/jalview/gui/AppVarnaBinding.java
index 8ab1e61..829fc3e 100644
--- a/src/jalview/gui/AppVarnaBinding.java
+++ b/src/jalview/gui/AppVarnaBinding.java
@@ -384,7 +384,7 @@ public class AppVarnaBinding extends JalviewVarnaBinding
   }
 
   @Override
-  public String[] getPdbFile()
+  public String[] getStructureFiles()
   {
     return null;
   }
diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index ab6f6c8..eadc2ad 100644
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -490,7 +490,7 @@ public class ChimeraViewFrame extends StructureViewerBase
     StructureFile pdb = null;
     try
     {
-      String[] curfiles = jmb.getPdbFile(); // files currently in viewer
+      String[] curfiles = jmb.getStructureFiles(); // files currently in viewer
       // TODO: replace with reference fetching/transfer code (validate PDBentry
       // as a DBRef?)
       for (int pi = 0; pi < jmb.getPdbCount(); pi++)
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index ab5bc49..494d690 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -577,6 +577,7 @@ public class SeqPanel extends JPanel implements MouseListener,
   @Override
   public void mouseReleased(MouseEvent evt)
   {
+    boolean didDrag = mouseDragging; // did we come here after a drag
     mouseDragging = false;
     mouseWheelPressed = false;
 
@@ -589,7 +590,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     if (!editingSeqs)
     {
-      doMouseReleasedDefineMode(evt);
+      doMouseReleasedDefineMode(evt, didDrag);
       return;
     }
 
@@ -1730,7 +1731,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     List<SequenceFeature> allFeatures = ap.getFeatureRenderer()
             .findFeaturesAtRes(sequence.getDatasetSequence(),
                     sequence.findPosition(res));
-    List<String> links = new ArrayList<String>();
+    List<String> links = new ArrayList<>();
     for (SequenceFeature sf : allFeatures)
     {
       if (sf.links != null)
@@ -1747,12 +1748,15 @@ public class SeqPanel extends JPanel implements MouseListener,
   }
 
   /**
-   * DOCUMENT ME!
+   * Update the display after mouse up on a selection or group
    * 
    * @param evt
-   *          DOCUMENT ME!
+   *          mouse released event details
+   * @param afterDrag
+   *          true if this event is happening after a mouse drag (rather than a
+   *          mouse down)
    */
-  public void doMouseReleasedDefineMode(MouseEvent evt)
+  public void doMouseReleasedDefineMode(MouseEvent evt, boolean afterDrag)
   {
     if (stretchGroup == null)
     {
@@ -1761,7 +1765,8 @@ public class SeqPanel extends JPanel implements MouseListener,
     // always do this - annotation has own state
     // but defer colourscheme update until hidden sequences are passed in
     boolean vischange = stretchGroup.recalcConservation(true);
-    needOverviewUpdate |= vischange && av.isSelectionDefinedGroup();
+    needOverviewUpdate |= vischange && av.isSelectionDefinedGroup()
+            && afterDrag;
     if (stretchGroup.cs != null)
     {
       stretchGroup.cs.alignmentChanged(stretchGroup,
@@ -2015,11 +2020,13 @@ public class SeqPanel extends JPanel implements MouseListener,
         ap.getCalculationDialog().validateCalcTypes();
       }
 
-      // process further ?
-      if (!av.followSelection)
-      {
-        return;
-      }
+      return;
+    }
+
+    // process further ?
+    if (!av.followSelection)
+    {
+      return;
     }
 
     /*
diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index e37627d..e73ce07 100644
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -919,7 +919,7 @@ 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 +991,7 @@ 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);
diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 7c6d181..9d5fd93 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -39,7 +39,10 @@ import jalview.json.binding.biojson.v1.ColourSchemeMapper;
 import jalview.schemes.ColourSchemeI;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
+import jalview.ws.utils.UrlDownloadClient;
 
+import java.io.File;
+import java.io.IOException;
 import java.util.StringTokenizer;
 import java.util.Vector;
 
@@ -205,6 +208,12 @@ public class FileLoader implements Runnable
       // refer to it as.
       return;
     }
+    if (file != null
+            && file.indexOf(System.getProperty("java.io.tmpdir")) > -1)
+    {
+      // ignore files loaded from the system's temporary directory
+      return;
+    }
     String type = protocol == DataSourceType.FILE ? "RECENT_FILE"
             : "RECENT_URL";
 
@@ -325,9 +334,27 @@ public class FileLoader implements Runnable
 
             // open a new source and read from it
             FormatAdapter fa = new FormatAdapter();
-            al = fa.readFile(file, protocol, format);
-            source = fa.getAlignFile(); // keep reference for later if
-                                        // necessary.
+            boolean downloadStructureFile = format.isStructureFile()
+                    && protocol.equals(DataSourceType.URL);
+            if (downloadStructureFile)
+            {
+              String structExt = format.getExtensions().split(",")[0];
+              String urlLeafName = file.substring(file.lastIndexOf(System
+                      .getProperty("file.separator")), file
+                      .lastIndexOf("."));
+              String tempStructureFileStr = createNamedJvTempFile(
+                      urlLeafName, structExt);
+              UrlDownloadClient.download(file, tempStructureFileStr);
+              al = fa.readFile(tempStructureFileStr, DataSourceType.FILE,
+                      format);
+              source = fa.getAlignFile();
+            }
+            else
+            {
+              al = fa.readFile(file, protocol, format);
+              source = fa.getAlignFile(); // keep reference for later if
+                                          // necessary.
+            }
           }
         } catch (java.io.IOException ex)
         {
@@ -556,6 +583,29 @@ public class FileLoader implements Runnable
 
   }
 
+  /**
+   * This method creates the file -
+   * {tmpdir}/jalview/{current_timestamp}/fileName.exetnsion using the supplied
+   * file name and extension
+   * 
+   * @param fileName
+   *          the name of the temp file to be created
+   * @param extension
+   *          the extension of the temp file to be created
+   * @return
+   */
+  private static String createNamedJvTempFile(String fileName,
+          String extension) throws IOException
+  {
+    String seprator = System.getProperty("file.separator");
+    String jvTempDir = System.getProperty("java.io.tmpdir") + "jalview"
+            + seprator + System.currentTimeMillis();
+    File tempStructFile = new File(jvTempDir + seprator + fileName + "."
+            + extension);
+    tempStructFile.mkdirs();
+    return tempStructFile.toString();
+  }
+
   /*
    * (non-Javadoc)
    * 
diff --git a/src/jalview/io/StructureFile.java b/src/jalview/io/StructureFile.java
index 7fe17c8..ab220f0 100644
--- a/src/jalview/io/StructureFile.java
+++ b/src/jalview/io/StructureFile.java
@@ -406,7 +406,8 @@ public abstract class StructureFile extends AlignFile
    * make a friendly ID string.
    * 
    * @param dataName
-   * @return truncated dataName to after last '/'
+   * @return truncated dataName to after last '/' and pruned .extension if
+   *         present
    */
   protected String safeName(String dataName)
   {
@@ -415,6 +416,9 @@ public abstract class StructureFile extends AlignFile
     {
       dataName = dataName.substring(p + 1);
     }
+    if(dataName.indexOf(".") > -1){
+      dataName = dataName.substring(0, dataName.lastIndexOf("."));
+    }
     return dataName;
   }
 
diff --git a/src/jalview/javascript/MouseOverStructureListener.java b/src/jalview/javascript/MouseOverStructureListener.java
index 7580222..c390b17 100644
--- a/src/jalview/javascript/MouseOverStructureListener.java
+++ b/src/jalview/javascript/MouseOverStructureListener.java
@@ -126,7 +126,7 @@ public class MouseOverStructureListener extends JSFunctionExec implements
   }
 
   @Override
-  public String[] getPdbFile()
+  public String[] getStructureFiles()
   {
     return modelSet;
   }
diff --git a/src/jalview/structure/StructureListener.java b/src/jalview/structure/StructureListener.java
index e5c5d04..9fde3f1 100644
--- a/src/jalview/structure/StructureListener.java
+++ b/src/jalview/structure/StructureListener.java
@@ -31,7 +31,7 @@ public interface StructureListener
    * handles messages for, or null if generic listener (only used by
    * removeListener method)
    */
-  public String[] getPdbFile();
+  public String[] getStructureFiles();
 
   /**
    * Called by StructureSelectionManager to inform viewer to highlight given
diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 72da7ae..db0b47e 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -36,6 +36,7 @@ import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceI;
 import jalview.ext.jmol.JmolParser;
 import jalview.gui.IProgressIndicator;
+import jalview.io.AppletFormatAdapter;
 import jalview.io.DataSourceType;
 import jalview.io.StructureFile;
 import jalview.util.MappingUtils;
@@ -385,6 +386,7 @@ public class StructureSelectionManager
     boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
     try
     {
+      sourceType = AppletFormatAdapter.checkProtocol(pdbFile);
       pdb = new JmolParser(pdbFile, sourceType);
 
       if (pdb.getId() != null && pdb.getId().trim().length() > 0
@@ -740,7 +742,7 @@ public class StructureSelectionManager
       if (listeners.elementAt(i) instanceof StructureListener)
       {
         sl = (StructureListener) listeners.elementAt(i);
-        for (String pdbfile : sl.getPdbFile())
+        for (String pdbfile : sl.getStructureFiles())
         {
           pdbs.remove(pdbfile);
         }
diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java
index b336e45..1637631 100644
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -532,7 +532,7 @@ public abstract class AAStructureBindingModel extends
           BitSet matched, SuperposeData[] structures)
   {
     int refStructure = -1;
-    String[] files = getPdbFile();
+    String[] files = getStructureFiles();
     if (files == null)
     {
       return -1;
@@ -756,7 +756,7 @@ public abstract class AAStructureBindingModel extends
     {
       return;
     }
-    String[] files = getPdbFile();
+    String[] files = getStructureFiles();
   
     SequenceRenderer sr = getSequenceRenderer(alignmentv);
   
diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index cdf0758..60cee46 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -92,9 +92,9 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   FeaturesDisplayedI featuresDisplayed = null;
 
-  protected Deque<CommandI> historyList = new ArrayDeque<CommandI>();
+  protected Deque<CommandI> historyList = new ArrayDeque<>();
 
-  protected Deque<CommandI> redoList = new ArrayDeque<CommandI>();
+  protected Deque<CommandI> redoList = new ArrayDeque<>();
 
   /**
    * alignment displayed in the viewport. Please use get/setter
@@ -1113,7 +1113,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
   public void setHiddenColumns(HiddenColumns hidden)
   {
     this.alignment.setHiddenColumns(hidden);
-    // this.colSel = colsel;
   }
 
   @Override
@@ -1298,7 +1297,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   protected boolean showOccupancy = true;
 
-  private Map<SequenceI, Color> sequenceColours = new HashMap<SequenceI, Color>();
+  private Map<SequenceI, Color> sequenceColours = new HashMap<>();
 
   protected SequenceAnnotationOrder sortAnnotationsBy = null;
 
@@ -1528,7 +1527,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
     if (hiddenRepSequences == null)
     {
-      hiddenRepSequences = new Hashtable<SequenceI, SequenceCollectionI>();
+      hiddenRepSequences = new Hashtable<>();
     }
 
     hiddenRepSequences.put(repSequence, sg);
@@ -1736,7 +1735,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   @Override
   public List<int[]> getVisibleRegionBoundaries(int min, int max)
   {
-    ArrayList<int[]> regions = new ArrayList<int[]>();
+    ArrayList<int[]> regions = new ArrayList<>();
     int start = min;
     int end = max;
 
@@ -1779,7 +1778,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   public List<AlignmentAnnotation> getVisibleAlignmentAnnotation(
           boolean selectedOnly)
   {
-    ArrayList<AlignmentAnnotation> ala = new ArrayList<AlignmentAnnotation>();
+    ArrayList<AlignmentAnnotation> ala = new ArrayList<>();
     AlignmentAnnotation[] aa;
     if ((aa = alignment.getAlignmentAnnotation()) != null)
     {
@@ -2133,7 +2132,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
     // intersect alignment annotation with alignment groups
 
     AlignmentAnnotation[] aan = alignment.getAlignmentAnnotation();
-    List<SequenceGroup> oldrfs = new ArrayList<SequenceGroup>();
+    List<SequenceGroup> oldrfs = new ArrayList<>();
     if (aan != null)
     {
       for (int an = 0; an < aan.length; an++)
@@ -2846,8 +2845,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
         selectionIsDefinedGroup = gps.contains(selectionGroup);
       }
     }
-    return selectionGroup.getContext() == alignment
-            || selectionIsDefinedGroup;
+    return selectionGroup.isDefined() || selectionIsDefinedGroup;
   }
 
   /**
diff --git a/src/jalview/ws/utils/UrlDownloadClient.java b/src/jalview/ws/utils/UrlDownloadClient.java
index 86e3f76..dcd861a 100644
--- a/src/jalview/ws/utils/UrlDownloadClient.java
+++ b/src/jalview/ws/utils/UrlDownloadClient.java
@@ -47,7 +47,8 @@ public class UrlDownloadClient
    *          the name of file to save the URLs to
    * @throws IOException
    */
-  public void download(String urlstring, String outfile) throws IOException
+  public static void download(String urlstring, String outfile)
+          throws IOException
   {
     FileOutputStream fos = null;
     ReadableByteChannel rbc = null;
diff --git a/test/jalview/datamodel/SequenceGroupTest.java b/test/jalview/datamodel/SequenceGroupTest.java
index 6e1c2db..f6d4028 100644
--- a/test/jalview/datamodel/SequenceGroupTest.java
+++ b/test/jalview/datamodel/SequenceGroupTest.java
@@ -3,12 +3,16 @@ package jalview.datamodel;
 import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertFalse;
 import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertNotSame;
 import static org.testng.Assert.assertNull;
 import static org.testng.Assert.assertSame;
 import static org.testng.Assert.assertTrue;
 import static org.testng.Assert.fail;
 
 import jalview.schemes.NucleotideColourScheme;
+import jalview.schemes.PIDColourScheme;
+
+import java.awt.Color;
 
 import junit.extensions.PA;
 
@@ -121,13 +125,32 @@ public class SequenceGroupTest
     PA.setValue(sg2, "context", sg2);
     try
     {
-      sg3.setContext(sg2); // circular reference in sg2
+      sg3.setContext(sg2, false); // circular reference in sg2
       fail("Expected exception");
     } catch (IllegalArgumentException e)
     {
       // expected
       assertNull(sg3.getContext());
     }
+
+    // test isDefined setting behaviour
+    sg2 = new SequenceGroup();
+    sg1.setContext(null, false);
+    assertFalse(sg1.isDefined());
+
+    sg1.setContext(sg2, false);
+    assertFalse(sg1.isDefined());
+
+    sg1.setContext(sg2, true);
+    assertTrue(sg1.isDefined());
+
+    // setContext without defined parameter does not change isDefined
+    sg1.setContext(null);
+    assertTrue(sg1.isDefined());
+
+    sg1.setContext(null, false);
+    sg1.setContext(sg2);
+    assertFalse(sg1.isDefined());
   }
 
   @Test(groups = { "Functional" })
@@ -198,6 +221,73 @@ public class SequenceGroupTest
     assertTrue(sg2.contains(seq2, 8));
     sg2.deleteSequence(seq2, false);
     assertFalse(sg2.contains(seq2));
+  }
+
+  @Test(groups = { "Functional" })
+  public void testCopyConstructor()
+  {
+    SequenceI seq = new Sequence("seq", "ABC");
+    SequenceGroup sg = new SequenceGroup();
+    sg.addSequence(seq, false);
+    sg.setName("g1");
+    sg.setDescription("desc");
+    sg.setColourScheme(new PIDColourScheme());
+    sg.setDisplayBoxes(false);
+    sg.setDisplayText(false);
+    sg.setColourText(true);
+    sg.isDefined = true;
+    sg.setShowNonconserved(true);
+    sg.setOutlineColour(Color.red);
+    sg.setIdColour(Color.blue);
+    sg.thresholdTextColour = 1;
+    sg.textColour = Color.orange;
+    sg.textColour2 = Color.yellow;
+    sg.setIgnoreGapsConsensus(false);
+    sg.setshowSequenceLogo(true);
+    sg.setNormaliseSequenceLogo(true);
+    sg.setHidereps(true);
+    sg.setHideCols(true);
+    sg.setShowConsensusHistogram(true);
+    sg.setContext(new SequenceGroup());
+
+    SequenceGroup sg2 = new SequenceGroup(sg);
+    assertEquals(sg2.getName(), sg.getName());
+    assertEquals(sg2.getDescription(), sg.getDescription());
+    assertNotSame(sg2.getGroupColourScheme(), sg.getGroupColourScheme());
+    assertSame(sg2.getColourScheme(), sg.getColourScheme());
+    assertEquals(sg2.getDisplayBoxes(), sg.getDisplayBoxes());
+    assertEquals(sg2.getDisplayText(), sg.getDisplayText());
+    assertEquals(sg2.getColourText(), sg.getColourText());
+    assertEquals(sg2.getShowNonconserved(), sg.getShowNonconserved());
+    assertEquals(sg2.getOutlineColour(), sg.getOutlineColour());
+    assertEquals(sg2.getIdColour(), sg.getIdColour());
+    assertEquals(sg2.thresholdTextColour, sg.thresholdTextColour);
+    assertEquals(sg2.textColour, sg.textColour);
+    assertEquals(sg2.textColour2, sg.textColour2);
+    assertEquals(sg2.getIgnoreGapsConsensus(), sg.getIgnoreGapsConsensus());
+    assertEquals(sg2.isShowSequenceLogo(), sg.isShowSequenceLogo());
+    assertEquals(sg2.isNormaliseSequenceLogo(),
+            sg.isNormaliseSequenceLogo());
+    assertEquals(sg2.isHidereps(), sg.isHidereps());
+    assertEquals(sg2.isHideCols(), sg.isHideCols());
+    assertEquals(sg2.isShowConsensusHistogram(),
+            sg.isShowConsensusHistogram());
+
+    /*
+     * copy of sequences
+     */
+    assertNotSame(sg2.getSequences(), sg.getSequences());
+    assertEquals(sg2.getSequences(), sg.getSequences());
 
+    /*
+     * isDefined should only be set true when a new group is added to
+     * an alignment, not in the copy constructor
+     */
+    assertFalse(sg2.isDefined());
+
+    /*
+     * context should be set explicitly, not by copy
+     */
+    assertNull(sg2.getContext());
   }
 }
diff --git a/test/jalview/ext/jmol/JmolViewerTest.java b/test/jalview/ext/jmol/JmolViewerTest.java
index 995b099..4a59044 100644
--- a/test/jalview/ext/jmol/JmolViewerTest.java
+++ b/test/jalview/ext/jmol/JmolViewerTest.java
@@ -33,6 +33,7 @@ import jalview.gui.StructureViewer;
 import jalview.gui.StructureViewer.ViewerType;
 import jalview.io.DataSourceType;
 
+import org.testng.Assert;
 import org.testng.annotations.AfterClass;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
@@ -115,4 +116,57 @@ public class JmolViewerTest
       }
     }
   }
+
+  @Test(groups = { "Functional", "Network" })
+  public void testStructureLoadingViaURL()
+  {
+    Cache.setProperty(Preferences.STRUCTURE_DISPLAY, ViewerType.JMOL.name());
+    String inFile = "http://www.jalview.org/builds/develop/examples/3W5V.pdb";
+    AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
+            inFile, DataSourceType.URL);
+    assertTrue("Didn't read input file " + inFile, af != null);
+    for (SequenceI sq : af.getViewport().getAlignment().getSequences())
+    {
+      SequenceI dsq = sq.getDatasetSequence();
+      while (dsq.getDatasetSequence() != null)
+      {
+        dsq = dsq.getDatasetSequence();
+      }
+      if (dsq.getAllPDBEntries() != null
+              && dsq.getAllPDBEntries().size() > 0)
+      {
+        for (int q = 0; q < dsq.getAllPDBEntries().size(); q++)
+        {
+          final StructureViewer structureViewer = new StructureViewer(af
+                  .getViewport().getStructureSelectionManager());
+          structureViewer.setViewerType(ViewerType.JMOL);
+          JalviewStructureDisplayI jmolViewer = structureViewer
+                  .viewStructures(dsq.getAllPDBEntries().elementAt(q),
+                          new SequenceI[] { sq }, af.getCurrentView()
+                                  .getAlignPanel());
+          /*
+          * Wait for viewer load thread to complete
+          */
+          try
+          {
+            while (!jmolViewer.getBinding().isFinishedInit())
+            {
+              Thread.sleep(500);
+            }
+          } catch (InterruptedException e)
+          {
+          }
+          // System.out.println(">>>>>>>>>>>>>>>>> "
+          // + jmolViewer.getBinding().getPdbFile());
+          String[] expectedModelFiles = new String[] { "http://www.jalview.org/builds/develop/examples/3W5V.pdb" };
+          String[] actualModelFiles = jmolViewer.getBinding().getStructureFiles();
+          Assert.assertEqualsNoOrder(actualModelFiles, expectedModelFiles);
+          jmolViewer.closeViewer(true);
+          // todo: break here means only once through this loop?
+          break;
+        }
+        break;
+      }
+    }
+  }
 }
diff --git a/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java b/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
index d85bb10..29fd092 100644
--- a/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
+++ b/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
@@ -217,7 +217,7 @@ public class JalviewChimeraView
      * (or possibly 52-145 to 1-94 - see JAL-2319)
      */
     StructureSelectionManager ssm = binding.getSsm();
-    String pdbFile = binding.getPdbFile()[0];
+    String pdbFile = binding.getStructureFiles()[0];
     StructureMapping[] mappings = ssm.getMapping(pdbFile);
     assertTrue(mappings[0].getMappingDetailsOutput().contains("SIFTS"),
             "Failed to perform SIFTS mapping");
diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java
index e6c16b7..4660842 100644
--- a/test/jalview/gui/AlignViewportTest.java
+++ b/test/jalview/gui/AlignViewportTest.java
@@ -160,7 +160,7 @@ public class AlignViewportTest
     acf2.addMap(s1, s1, new MapList(new int[] { 1, 4 }, new int[] { 4, 1 },
             1, 1));
 
-    List<AlignedCodonFrame> mappings = new ArrayList<AlignedCodonFrame>();
+    List<AlignedCodonFrame> mappings = new ArrayList<>();
     mappings.add(acf1);
     mappings.add(acf2);
     af1.getViewport().getAlignment().setCodonFrames(mappings);
@@ -217,11 +217,11 @@ public class AlignViewportTest
     acf3.addMap(cs2, cs2, new MapList(new int[] { 1, 12 }, new int[] { 1,
         12 }, 1, 1));
 
-    List<AlignedCodonFrame> mappings1 = new ArrayList<AlignedCodonFrame>();
+    List<AlignedCodonFrame> mappings1 = new ArrayList<>();
     mappings1.add(acf1);
     af1.getViewport().getAlignment().setCodonFrames(mappings1);
 
-    List<AlignedCodonFrame> mappings2 = new ArrayList<AlignedCodonFrame>();
+    List<AlignedCodonFrame> mappings2 = new ArrayList<>();
     mappings2.add(acf2);
     mappings2.add(acf3);
     af2.getViewport().getAlignment().setCodonFrames(mappings2);
@@ -280,12 +280,12 @@ public class AlignViewportTest
     acf3.addMap(cs2, cs2, new MapList(new int[] { 1, 12 }, new int[] { 1,
         12 }, 1, 1));
 
-    List<AlignedCodonFrame> mappings1 = new ArrayList<AlignedCodonFrame>();
+    List<AlignedCodonFrame> mappings1 = new ArrayList<>();
     mappings1.add(acf1);
     mappings1.add(acf2);
     af1.getViewport().getAlignment().setCodonFrames(mappings1);
 
-    List<AlignedCodonFrame> mappings2 = new ArrayList<AlignedCodonFrame>();
+    List<AlignedCodonFrame> mappings2 = new ArrayList<>();
     mappings2.add(acf2);
     mappings2.add(acf3);
     af2.getViewport().getAlignment().setCodonFrames(mappings2);
@@ -389,7 +389,8 @@ public class AlignViewportTest
 
   /**
    * Verify that setting the selection group has the side-effect of setting the
-   * context on the group, unless it already has one
+   * context on the group, unless it already has one, but does not change
+   * whether the group is defined or not.
    */
   @Test(groups = { "Functional" })
   public void testSetSelectionGroup()
@@ -399,13 +400,21 @@ public class AlignViewportTest
     AlignViewport av = af.getViewport();
     SequenceGroup sg1 = new SequenceGroup();
     SequenceGroup sg2 = new SequenceGroup();
+    SequenceGroup sg3 = new SequenceGroup();
 
     av.setSelectionGroup(sg1);
     assertSame(sg1.getContext(), av.getAlignment()); // context set
+    assertFalse(sg1.isDefined()); // group not defined
 
-    sg2.setContext(sg1);
+    sg2.setContext(sg1, false);
     av.setSelectionGroup(sg2);
+    assertFalse(sg2.isDefined()); // unchanged
     assertSame(sg2.getContext(), sg1); // unchanged
+
+    // create a defined group
+    sg3.setContext(av.getAlignment(), true);
+    av.setSelectionGroup(sg3);
+    assertTrue(sg3.isDefined()); // unchanged
   }
   /**
    * Verify that setting/clearing SHOW_OCCUPANCY preference adds or omits occupancy row from viewport
diff --git a/test/jalview/io/FileLoaderTest.java b/test/jalview/io/FileLoaderTest.java
new file mode 100644
index 0000000..0e21f6e
--- /dev/null
+++ b/test/jalview/io/FileLoaderTest.java
@@ -0,0 +1,24 @@
+package jalview.io;
+
+import org.junit.Assert;
+import org.testng.annotations.Test;
+
+public class FileLoaderTest
+{
+
+  @Test(groups = { "Network" })
+  public void testDownloadStructuresIfInputFromURL()
+  {
+    String urlFile = "http://www.jalview.org/builds/develop/examples/3W5V.pdb";
+    FileLoader fileLoader = new FileLoader();
+    fileLoader.LoadFileWaitTillLoaded(urlFile, DataSourceType.URL,
+            FileFormat.PDB);
+    Assert.assertNotNull(fileLoader.file);
+    // The FileLoader's file is expected to a temporary file different from the
+    // original URL.
+    Assert.assertNotEquals(urlFile, fileLoader.file);
+    // Data source type expected to be updated from DataSourceType.URL to
+    // DataSourceType.FILE
+    Assert.assertEquals(DataSourceType.FILE, fileLoader.protocol);
+  }
+}
diff --git a/test/jalview/structures/models/AAStructureBindingModelTest.java b/test/jalview/structures/models/AAStructureBindingModelTest.java
index a7e483e..c125ef6 100644
--- a/test/jalview/structures/models/AAStructureBindingModelTest.java
+++ b/test/jalview/structures/models/AAStructureBindingModelTest.java
@@ -138,7 +138,7 @@ public class AAStructureBindingModelTest
     testee = new AAStructureBindingModel(ssm, pdbFiles, seqs, null)
     {
       @Override
-      public String[] getPdbFile()
+      public String[] getStructureFiles()
       {
         return new String[] { "INLINE1YCS", "INLINE3A6S", "INLINE1OOT" };
       }
@@ -230,7 +230,7 @@ public class AAStructureBindingModelTest
     /*
      * create a data bean to hold data per structure file
      */
-    SuperposeData[] structs = new SuperposeData[testee.getPdbFile().length];
+    SuperposeData[] structs = new SuperposeData[testee.getStructureFiles().length];
     for (int i = 0; i < structs.length; i++)
     {
       structs[i] = testee.new SuperposeData(al.getWidth());