JAL-2602 check for null or empty description when copying consensus

[jalview.git] / src / jalview / io / FileLoader.java

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 8b753e6..9d5fd93 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -27,7 +27,7 @@ import jalview.api.FeaturesSourceI;
 import jalview.bin.Cache;
 import jalview.bin.Jalview;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
@@ -208,6 +208,12 @@ public class FileLoader implements Runnable
       // refer to it as.
       return;
     }
+    if (file != null
+            && file.indexOf(System.getProperty("java.io.tmpdir")) > -1)
+    {
+      // ignore files loaded from the system's temporary directory
+      return;
+    }
     String type = protocol == DataSourceType.FILE ? "RECENT_FILE"
             : "RECENT_URL";
 
@@ -339,12 +345,16 @@ public class FileLoader implements Runnable
               String tempStructureFileStr = createNamedJvTempFile(
                       urlLeafName, structExt);
               UrlDownloadClient.download(file, tempStructureFileStr);
-              file = tempStructureFileStr;
-              protocol = DataSourceType.FILE;
+              al = fa.readFile(tempStructureFileStr, DataSourceType.FILE,
+                      format);
+              source = fa.getAlignFile();
+            }
+            else
+            {
+              al = fa.readFile(file, protocol, format);
+              source = fa.getAlignFile(); // keep reference for later if
+                                          // necessary.
             }
-            al = fa.readFile(file, protocol, format);
-            source = fa.getAlignFile(); // keep reference for later if
-                                        // necessary.
           }
         } catch (java.io.IOException ex)
         {
@@ -389,8 +399,8 @@ public class FileLoader implements Runnable
 
             if (source instanceof ComplexAlignFile)
             {
-              ColumnSelection colSel = ((ComplexAlignFile) source)
-                      .getColumnSelection();
+              HiddenColumns colSel = ((ComplexAlignFile) source)
+                      .getHiddenColumns();
               SequenceI[] hiddenSeqs = ((ComplexAlignFile) source)
                       .getHiddenSequences();
               String colourSchemeName = ((ComplexAlignFile) source)