made PhyloInferenceDialog constructor refer to null instead of mainframe

[jalview.git] / forester / java / src / org / forester / archaeopteryx / tools / SequenceDataRetriver.java

diff --git a/forester/java/src/org/forester/archaeopteryx/tools/SequenceDataRetriver.java b/forester/java/src/org/forester/archaeopteryx/tools/SequenceDataRetriver.java
index 9f3bcb1..1cd6b54 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/tools/SequenceDataRetriver.java
+++ b/forester/java/src/org/forester/archaeopteryx/tools/SequenceDataRetriver.java
@@ -38,11 +38,10 @@ import org.forester.ws.seqdb.SequenceDbWsTools;
 
 public final class SequenceDataRetriver extends RunnableProcess {
 
-    private final static int           DEFAULT_LINES_TO_RETURN = 4000;
     private final Phylogeny            _phy;
     private final MainFrameApplication _mf;
     private final TreePanel            _treepanel;
-    public final static boolean        DEBUG                   = false;
+    public final static boolean        DEBUG = false;
 
     public SequenceDataRetriver( final MainFrameApplication mf, final TreePanel treepanel, final Phylogeny phy ) {
         _phy = phy;
@@ -59,7 +58,10 @@ public final class SequenceDataRetriver extends RunnableProcess {
         start( _mf, "sequence data" );
         SortedSet<String> not_found = null;
         try {
-            not_found = SequenceDbWsTools.obtainSeqInformation( _phy, false, true, DEFAULT_LINES_TO_RETURN );
+            not_found = SequenceDbWsTools.obtainSeqInformation( _phy,
+                                                                false,
+                                                                true,
+                                                                SequenceDbWsTools.DEFAULT_LINES_TO_RETURN );
         }
         catch ( final UnknownHostException e ) {
             JOptionPane.showMessageDialog( _mf,
@@ -91,11 +93,10 @@ public final class SequenceDataRetriver extends RunnableProcess {
             }
             final StringBuffer sb = new StringBuffer();
             if ( not_found.size() == 1 ) {
-                sb.append( "Data for the following sequence identifier was not found:\n" );
+                sb.append( "For the following node no data was found:\n" );
             }
             else {
-                sb.append( "Data for the following sequence identifiers was not found (total: " + not_found.size()
-                        + "):\n" );
+                sb.append( "For the following nodes no data was found (total: " + not_found.size() + "):\n" );
             }
             int i = 0;
             for( final String string : not_found ) {
@@ -116,7 +117,7 @@ public final class SequenceDataRetriver extends RunnableProcess {
                                                JOptionPane.WARNING_MESSAGE );
             }
             catch ( final Exception e ) {
-                // Not important if this fails, do nothing. 
+                // Not important if this fails, do nothing.
             }
         }
         else {