X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fproject%2FJalview2XML.java;h=d4b2c047eb240d39e696faaef134f63dcaf05ca0;hb=679d96501d13df061a2bc1b6cb9757256253d267;hp=8877af2941b735e5bcccfa938e3cf7a6c0967b8c;hpb=cb8e52fbbc5f725e3f7f48c672cdddb0690bd978;p=jalview.git

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index 8877af2..d4b2c04 100644
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -882,8 +882,7 @@ public class Jalview2XML
     {
       System.err.println("error writing date: " + e.toString());
     }
-    object.setVersion(
-            Cache.getDefault("VERSION", "Development Build"));
+    object.setVersion(Cache.getDefault("VERSION", "Development Build"));
 
     /**
      * rjal is full height alignment, jal is actual alignment with full metadata
@@ -1633,7 +1632,8 @@ public class Jalview2XML
                 .getHiddenColumns();
         if (hidden == null)
         {
-          Console.warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
+          Console.warn(
+                  "REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
         }
         else
         {
@@ -2418,7 +2418,8 @@ public class Jalview2XML
       }
       else
       {
-        Console.warn("Cannot resolve a service for the parameters used in this project. Try configuring a JABAWS server.");
+        Console.warn(
+                "Cannot resolve a service for the parameters used in this project. Try configuring a JABAWS server.");
         return false;
       }
     }
@@ -2462,7 +2463,8 @@ public class Jalview2XML
         return id.toString();
       }
       // give up and warn that something has gone wrong
-      Console.warn("Cannot find ID for object in external mapping : " + jvobj);
+      Console.warn(
+              "Cannot find ID for object in external mapping : " + jvobj);
     }
     return altCode;
   }
@@ -3230,7 +3232,8 @@ public class Jalview2XML
       }
       else
       {
-        Console.warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
+        Console.warn(
+                "Couldn't find entry in Jalview Jar for " + jarEntryName);
       }
     } catch (Exception ex)
     {
@@ -4205,8 +4208,9 @@ public class Jalview2XML
         tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews());
         if (tp == null)
         {
-          Console.warn("There was a problem recovering stored Newick tree: \n"
-                  + tree.getNewick());
+          Console.warn(
+                  "There was a problem recovering stored Newick tree: \n"
+                          + tree.getNewick());
           continue;
         }
 
@@ -5282,14 +5286,16 @@ public class Jalview2XML
       {
         if (ds != null && ds != seqSetDS)
         {
-          Console.warn("JAL-3171 regression: Overwriting a dataset reference for an alignment"
-                  + " - CDS/Protein crossreference data may be lost");
+          Console.warn(
+                  "JAL-3171 regression: Overwriting a dataset reference for an alignment"
+                          + " - CDS/Protein crossreference data may be lost");
           if (xtant_ds != null)
           {
             // This can only happen if the unique sequence set ID was bound to a
             // dataset that did not contain any of the sequences in the view
             // currently being restored.
-            Console.warn("JAL-3171 SERIOUS!  TOTAL CONFUSION - please consider contacting the Jalview Development team so they can investigate why your project caused this message to be displayed.");
+            Console.warn(
+                    "JAL-3171 SERIOUS!  TOTAL CONFUSION - please consider contacting the Jalview Development team so they can investigate why your project caused this message to be displayed.");
           }
         }
         ds = seqSetDS;
@@ -5573,7 +5579,8 @@ public class Jalview2XML
   {
     if (dataset.getDataset() != null)
     {
-      Console.warn("Serious issue!  Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
+      Console.warn(
+              "Serious issue!  Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
     }
     String datasetId = makeHashCode(dataset, null);
     if (datasetId == null)
@@ -5905,7 +5912,8 @@ public class Jalview2XML
       }
       else
       {
-        Console.warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
+        Console.warn(
+                "Couldn't find entry in Jalview Jar for " + jarEntryName);
       }
     } catch (Exception ex)
     {