JAL-915 - ensured that exceptions are not raised in applet or application, and that...

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index c202fd2..5d05ec3 100755 (executable)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -169,7 +169,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
       remove(groupMenu);
     }
 
-    if (links != null && links.size() > 0)
+    if (seq!=null && links != null && links.size() > 0)
     {
       Menu linkMenu = new Menu("Link");
       String link;
@@ -185,7 +185,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
         final String target = urlLink.getTarget(); // link.substring(0,
         // link.indexOf("|"));
         final String label = urlLink.getLabel();
-        if (urlLink.isDynamic())
+        if (seq!=null && urlLink.isDynamic())
         {
 
           // collect matching db-refs

diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index 402a8bf..a3955c0 100755 (executable)
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -89,61 +89,62 @@ public class IdPanel extends Panel implements MouseListener,
 
     // look for non-pos features
     StringBuffer tooltiptext = new StringBuffer();
-
-    if (sequence.getDescription() != null)
+    if (sequence != null)
     {
-      tooltiptext.append(sequence.getDescription());
-      tooltiptext.append("\n");
-    }
+      if (sequence.getDescription() != null)
+      {
+        tooltiptext.append(sequence.getDescription());
+        tooltiptext.append("\n");
+      }
 
-    SequenceFeature sf[] = sequence.getSequenceFeatures();
-    for (int sl = 0; sf != null && sl < sf.length; sl++)
-    {
-      if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
+      SequenceFeature sf[] = sequence.getSequenceFeatures();
+      for (int sl = 0; sf != null && sl < sf.length; sl++)
       {
-        boolean nl = false;
-        if (sf[sl].getFeatureGroup() != null)
-        {
-          tooltiptext.append(sf[sl].getFeatureGroup());
-          nl = true;
-        }
-        ;
-        if (sf[sl].getType() != null)
-        {
-          tooltiptext.append(" ");
-          tooltiptext.append(sf[sl].getType());
-          nl = true;
-        }
-        ;
-        if (sf[sl].getDescription() != null)
-        {
-          tooltiptext.append(" ");
-          tooltiptext.append(sf[sl].getDescription());
-          nl = true;
-        }
-        ;
-        if (sf[sl].getScore() != Float.NaN && sf[sl].getScore() != 0f)
-        {
-          tooltiptext.append(" Score = ");
-          tooltiptext.append(sf[sl].getScore());
-          nl = true;
-        }
-        ;
-        if (sf[sl].getStatus() != null && sf[sl].getStatus().length() > 0)
-        {
-          tooltiptext.append(" (");
-          tooltiptext.append(sf[sl].getStatus());
-          tooltiptext.append(")");
-          nl = true;
-        }
-        ;
-        if (nl)
+        if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
         {
-          tooltiptext.append("\n");
+          boolean nl = false;
+          if (sf[sl].getFeatureGroup() != null)
+          {
+            tooltiptext.append(sf[sl].getFeatureGroup());
+            nl = true;
+          }
+          ;
+          if (sf[sl].getType() != null)
+          {
+            tooltiptext.append(" ");
+            tooltiptext.append(sf[sl].getType());
+            nl = true;
+          }
+          ;
+          if (sf[sl].getDescription() != null)
+          {
+            tooltiptext.append(" ");
+            tooltiptext.append(sf[sl].getDescription());
+            nl = true;
+          }
+          ;
+          if (sf[sl].getScore() != Float.NaN && sf[sl].getScore() != 0f)
+          {
+            tooltiptext.append(" Score = ");
+            tooltiptext.append(sf[sl].getScore());
+            nl = true;
+          }
+          ;
+          if (sf[sl].getStatus() != null && sf[sl].getStatus().length() > 0)
+          {
+            tooltiptext.append(" (");
+            tooltiptext.append(sf[sl].getStatus());
+            tooltiptext.append(")");
+            nl = true;
+          }
+          ;
+          if (nl)
+          {
+            tooltiptext.append("\n");
+          }
         }
       }
     }
-
     if (tooltiptext.length() == 0)
     {
       // nothing to display - so clear tooltip if one is visible
@@ -196,7 +197,12 @@ public class IdPanel extends Panel implements MouseListener,
 
     // DEFAULT LINK IS FIRST IN THE LINK LIST
     int seq = alignPanel.seqPanel.findSeq(e);
-    String id = av.getAlignment().getSequenceAt(seq).getName();
+    SequenceI sq = av.getAlignment().getSequenceAt(seq);
+    if (sq==null)
+    {
+      return;
+    }
+    String id = sq.getName();
 
     String target = null;
     String url = null;
@@ -290,6 +296,7 @@ public class IdPanel extends Panel implements MouseListener,
     if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
     {
       Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq);
+      
       // build a new links menu based on the current links + any non-positional
       // features
       Vector nlinks = new Vector();
@@ -297,7 +304,7 @@ public class IdPanel extends Panel implements MouseListener,
       {
         nlinks.addElement(links.elementAt(l));
       }
-      SequenceFeature sf[] = sq.getSequenceFeatures();
+      SequenceFeature sf[] = sq==null ? null:sq.getSequenceFeatures();
       for (int sl = 0; sf != null && sl < sf.length; sl++)
       {
         if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
@@ -363,7 +370,7 @@ public class IdPanel extends Panel implements MouseListener,
       end = tmp;
       lastid = end;
     }
-    if (av.getSelectionGroup()==null)
+    if (av.getSelectionGroup() == null)
     {
       av.setSelectionGroup(new SequenceGroup());
     }

diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 5b689bf..ea8b711 100755 (executable)
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -314,7 +314,7 @@ public class IdPanel extends JPanel implements MouseListener,
       // build a new links menu based on the current links + any non-positional
       // features
       Vector nlinks = new Vector(Preferences.sequenceURLLinks);
-      SequenceFeature sf[] = sq.getDatasetSequence().getSequenceFeatures();
+      SequenceFeature sf[] = sq==null ? null : sq.getDatasetSequence().getSequenceFeatures();
       for (int sl = 0; sf != null && sl < sf.length; sl++)
       {
         if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 477136f..ca6b199 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -208,11 +208,11 @@ public class PopupMenu extends JPopupMenu
       e.printStackTrace();
     }
 
+    JMenuItem menuItem;
     if (seq != null)
     {
       sequenceMenu.setText(sequence.getName());
 
-      JMenuItem menuItem;
       if (seq.getDatasetSequence().getPDBId() != null
               && seq.getDatasetSequence().getPDBId().size() > 0)
       {
@@ -297,7 +297,11 @@ public class PopupMenu extends JPopupMenu
           });
           add(menuItem);
         }
-
+      }
+    }
+    // for the case when no sequences are even visible
+    if (ap.av.hasHiddenRows) {
+      {
         menuItem = new JMenuItem("Reveal All");
         menuItem.addActionListener(new ActionListener()
         {
@@ -318,7 +322,7 @@ public class PopupMenu extends JPopupMenu
 
     SequenceGroup sg = ap.av.getSelectionGroup();
 
-    if (sg != null)
+    if (sg != null&& sg.getSize()>0)
     {
       groupName.setText("Name: "+sg.getName());
       groupName.setText("Edit name and description of current group.");
@@ -431,7 +435,7 @@ public class PopupMenu extends JPopupMenu
       structureMenu.setVisible(false);
     }
 
-    if (links != null && links.size() > 0)
+    if (seq !=null && links != null && links.size() > 0)
     {
 
       JMenu linkMenu = new JMenu("Link");