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

Conflicts:
	src/jalview/appletgui/IdPanel.java
	src/jalview/gui/FeatureRenderer.java

diff --cc src/jalview/appletgui/IdPanel.java
index 80f03a1,4cc4a3a..39a15b8
--- 1/src/jalview/appletgui/IdPanel.java
--- 2/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@@ -55,11 -57,11 +56,11 @@@ public class IdPanel extends Panel impl
  
    UrlProviderI urlProvider = null;
  
--  public IdPanel(AlignViewport av, AlignmentPanel parent)
++  public IdPanel(AlignViewport viewport, AlignmentPanel parent)
    {
--    this.av = av;
++    this.av = viewport;
      alignPanel = parent;
--    idCanvas = new IdCanvas(av);
++    idCanvas = new IdCanvas(viewport);
      setLayout(new BorderLayout());
      add(idCanvas, BorderLayout.CENTER);
      idCanvas.addMouseListener(this);
@@@ -70,12 -72,12 +71,12 @@@
  
      // make a list of label,url pairs
      HashMap<String, String> urlList = new HashMap<String, String>();
--    if (av.applet != null)
++    if (viewport.applet != null)
      {
        for (int i = 1; i < 10; i++)
        {
--        label = av.applet.getParameter("linkLabel_" + i);
--        url = av.applet.getParameter("linkURL_" + i);
++        label = viewport.applet.getParameter("linkLabel_" + i);
++        url = viewport.applet.getParameter("linkURL_" + i);
  
          // only add non-null parameters
          if (label != null)
@@@ -87,7 -89,7 +88,7 @@@
        if (!urlList.isEmpty())
        {
          // set default as first entry in list
--        String defaultUrl = av.applet.getParameter("linkLabel_1");
++        String defaultUrl = viewport.applet.getParameter("linkLabel_1");
          UrlProviderFactoryI factory = new AppletUrlProviderFactory(
                  defaultUrl, urlList);
          urlProvider = factory.createUrlProvider();
@@@ -275,21 -288,30 +280,29 @@@
  
      if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
      {
 -      Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq);
 +      SequenceI sq = av.getAlignment().getSequenceAt(seq);
  
 -      // build a new links menu based on the current links + any non-positional
 -      // features
 +      /*
 +       *  build a new links menu based on the current links
 +       *  and any non-positional features
 +       */
-       List<String> nlinks = urlProvider.getLinksForMenu();
+       List<String> nlinks;
+       if (urlProvider != null)
+       {
+         nlinks = urlProvider.getLinksForMenu();
+       }
+       else
+       {
+         nlinks = new ArrayList<String>();
+       }
 -      SequenceFeature sf[] = sq == null ? null : sq.getSequenceFeatures();
 -      for (int sl = 0; sf != null && sl < sf.length; sl++)
 +
 +      for (SequenceFeature sf : sq.getFeatures().getNonPositionalFeatures())
        {
 -        if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
 +        if (sf.links != null)
          {
 -          if (sf[sl].links != null && sf[sl].links.size() > 0)
 +          for (String link : sf.links)
            {
 -            for (int l = 0, lSize = sf[sl].links.size(); l < lSize; l++)
 -            {
 -              nlinks.add(sf[sl].links.elementAt(l));
 -            }
 +            nlinks.add(link);
            }
          }
        }
@@@ -402,9 -424,9 +415,9 @@@
  
      boolean up = true;
  
--    public ScrollThread(boolean up)
++    public ScrollThread(boolean isUp)
      {
--      this.up = up;
++      this.up = isUp;
        start();
      }
  

diff --cc src/jalview/gui/FeatureRenderer.java
index 56da67c,50a8689..b33ada2
--- 1/src/jalview/gui/FeatureRenderer.java
--- 2/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@@ -42,7 -43,7 +43,8 @@@ import java.awt.event.MouseAdapter
  import java.awt.event.MouseEvent;
  import java.util.Arrays;
  import java.util.Comparator;
 +import java.util.HashMap;
+ import java.util.List;
  
  import javax.swing.JColorChooser;
  import javax.swing.JComboBox;
@@@ -358,47 -402,30 +403,56 @@@ public class FeatureRenderer extend
        }
        else if (reply == JvOptionPane.YES_OPTION)
        {
+         /*
+          * YES_OPTION corresponds to the Amend button
+          */
+         boolean typeChanged = !lastFeatureAdded.equals(sf.type);
 -        sf.type = lastFeatureAdded;
 -        sf.featureGroup = lastFeatureGroupAdded;
 -        sf.description = lastDescriptionAdded;
 -
 -        setColour(sf.type, fcol);
 -        getFeaturesDisplayed().setVisible(sf.type);
 -
 +        String newType = lastFeatureAdded;
 +        String newFeatureGroup = lastFeatureGroupAdded;
 +        String newDescription = lastDescriptionAdded;
 +
 +        setColour(newType, fcol);
 +        getFeaturesDisplayed().setVisible(newType);
 +        int newBegin = sf.begin;
 +        int newEnd = sf.end;
          try
          {
 -          sf.begin = ((Integer) start.getValue()).intValue();
 -          sf.end = ((Integer) end.getValue()).intValue();
 +          newBegin = ((Integer) start.getValue()).intValue();
 +          newEnd = ((Integer) end.getValue()).intValue();
          } catch (NumberFormatException ex)
          {
 +          // JSpinner doesn't accept invalid format data :-)
 +        }
 +
 +        /*
 +         * replace the feature by deleting it and adding a new one
 +         * (to ensure integrity of SequenceFeatures data store)
 +         */
-         sequences[0].deleteFeature(sf);
++        sequences.get(0).deleteFeature(sf);
 +        SequenceFeature newSf = new SequenceFeature(newType,
 +                newDescription, newBegin, newEnd, sf.getScore(),
 +                newFeatureGroup);
 +        // ensure any additional properties are copied
 +        if (sf.otherDetails != null)
 +        {
 +          newSf.otherDetails = new HashMap<String, Object>(sf.otherDetails);
 +        }
 +        ffile.parseDescriptionHTML(newSf, false);
 +        // add any additional links not parsed from description
 +        if (sf.links != null)
 +        {
 +          for (String link : sf.links)
 +          {
 +            newSf.addLink(link);
 +          }
          }
 +        // amend features only gets one sequence to act on
-         sequences[0].addSequenceFeature(newSf);
++        sequences.get(0).addSequenceFeature(newSf);
+ 
 -        ffile.parseDescriptionHTML(sf, false);
+         if (typeChanged)
+         {
+           findAllFeatures();
+         }
        }
      }
      else