JAL-4059 Revert libjs/MiGLayout as new miglayout transpile of 4.0 includes reference...

[jalview.git] / src / jalview / gui / CrossRefAction.java

diff --git a/src/jalview/gui/CrossRefAction.java b/src/jalview/gui/CrossRefAction.java
index 2ada4d2..9580ef8 100644 (file)
--- a/src/jalview/gui/CrossRefAction.java
+++ b/src/jalview/gui/CrossRefAction.java
@@ -20,11 +20,18 @@
  */
 package jalview.gui;
 
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
 import jalview.analysis.AlignmentUtils;
 import jalview.analysis.CrossRef;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureSettingsModelI;
 import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
@@ -36,18 +43,14 @@ import jalview.ext.ensembl.EnsemblMap;
 import jalview.io.gff.SequenceOntologyI;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.DBRefUtils;
+import jalview.util.IdUtils;
+import jalview.util.IdUtils.IdType;
 import jalview.util.MapList;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
 import jalview.ws.SequenceFetcher;
 
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
 /**
  * Factory constructor and runnable for discovering and displaying
  * cross-references for a set of aligned sequences
@@ -75,10 +78,10 @@ public class CrossRefAction implements Runnable
   @Override
   public void run()
   {
-    final long sttime = System.currentTimeMillis();
+    final long id = IdUtils.newId(IdType.PROGRESS);
     alignFrame.setProgressBar(MessageManager.formatMessage(
             "status.searching_for_sequences_from", new Object[]
-            { source }), sttime);
+            { source }), id);
     try
     {
       AlignmentI alignment = alignFrame.getViewport().getAlignment();
@@ -114,7 +117,8 @@ public class CrossRefAction implements Runnable
 
       if (dna && AlignmentUtils.looksLikeEnsembl(alignment))
       {
-        // override default featureColourScheme so products have Ensembl variant colours
+        // override default featureColourScheme so products have Ensembl variant
+        // colours
         featureColourScheme = new SequenceFetcher()
                 .getFeatureColourScheme(DBRefSource.ENSEMBL);
       }
@@ -205,7 +209,8 @@ public class CrossRefAction implements Runnable
        * and for JAL-3330 also to original alignFrame view(s)
        * this currently trashes any original settings.
        */
-      for (AlignmentViewPanel origpanel: alignFrame.getAlignPanels()) {
+      for (AlignmentViewPanel origpanel : alignFrame.getAlignPanels())
+      {
         origpanel.getAlignViewport()
                 .mergeFeaturesStyle(featureColourScheme);
       }
@@ -229,12 +234,12 @@ public class CrossRefAction implements Runnable
       new OOMWarning("whilst fetching crossreferences", e);
     } catch (Throwable e)
     {
-      Cache.log.error("Error when finding crossreferences", e);
+      Console.error("Error when finding crossreferences", e);
     } finally
     {
       alignFrame.setProgressBar(MessageManager.formatMessage(
               "status.finished_searching_for_sequences_from", new Object[]
-              { source }), sttime);
+              { source }), id);
     }
   }
 
@@ -292,9 +297,9 @@ public class CrossRefAction implements Runnable
     {
       return;
     }
-    
+
     Set<String> ensemblDivisions = new EnsemblInfo().getDivisions();
-    
+
     /*
      * first look for direct dbrefs from sequence to Ensembl
      */
@@ -429,7 +434,7 @@ public class CrossRefAction implements Runnable
                 MessageManager.getString("label.cant_map_cds"),
                 MessageManager.getString("label.operation_failed"),
                 JvOptionPane.OK_OPTION);
-        System.err.println("Failed to make CDS alignment");
+        jalview.bin.Console.errPrintln("Failed to make CDS alignment");
         return null;
       }
 
@@ -450,8 +455,7 @@ public class CrossRefAction implements Runnable
       copyAlignment = AlignmentUtils.makeCopyAlignment(sel,
               xrefs.getSequencesArray(), dataset);
     }
-    copyAlignment
-            .setGapCharacter(alignFrame.viewport.getGapCharacter());
+    copyAlignment.setGapCharacter(alignFrame.viewport.getGapCharacter());
 
     StructureSelectionManager ssm = StructureSelectionManager
             .getStructureSelectionManager(Desktop.instance);
@@ -464,8 +468,8 @@ public class CrossRefAction implements Runnable
 
     if (copyAlignment.getHeight() <= 0)
     {
-      System.err.println(
-              "No Sequences generated for xRef type " + source);
+      jalview.bin.Console
+              .errPrintln("No Sequences generated for xRef type " + source);
       return null;
     }