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[jalview.git] / src / jalview / analysis / Connectivity.java

diff --git a/src/jalview/analysis/Connectivity.java b/src/jalview/analysis/Connectivity.java
index 0f849e3..0df1145 100644 (file)
--- a/src/jalview/analysis/Connectivity.java
+++ b/src/jalview/analysis/Connectivity.java
@@ -23,9 +23,14 @@ package jalview.analysis;
 //import jalview.datamodel.AlignmentView;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
+import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
 import jalview.viewmodel.AlignmentViewport;
 
+import java.util.Comparator;
 import java.util.Hashtable;
+import java.util.HashSet;
+import java.util.TreeSet;
 
 /**
  * @Author MorellThomas
@@ -58,6 +63,7 @@ public class Connectivity
        int iOld = connectivity.get(sequences[i]);
        int jOld = connectivity.get(sequences[j]); 
         // count the connection if its score is not NaN
+//System.out.println(String.format("%s - %s : %f", sequences[i].getName(), sequences[j].getName(), scores[i][j]));
        if (!Float.isNaN(scores[i][j]))
        {
          connectivity.put(sequences[i], ++iOld);
@@ -72,7 +78,7 @@ public class Connectivity
       System.out.println(String.format("%s: %d", sequence.getName(), connection));
       if (connection < dim)
       {
-       // a popup saying that it failed would be nice
+       JvOptionPane.showInternalMessageDialog(Desktop.desktop, String.format("Insufficient number of connections for %s (%d, should be %d or more)", sequence.getName(), connection, dim), "Connectivity Error", JvOptionPane.WARNING_MESSAGE);
        throw new ConnectivityException(sequence.getName(), connection, dim);
       }
     } );