Merge remote-tracking branch 'origin/releases/Release_2_10_2b1_Branch'

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

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 907ff46..5e209e6 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -85,8 +85,9 @@ public class AppletFormatAdapter
   public static String getSupportedFormats()
   {
     return "Formats currently supported are\n"
-          + prettyPrint(FileFormats.getInstance().getReadableFormats());
+            + prettyPrint(FileFormats.getInstance().getReadableFormats());
   }
+
   public AppletFormatAdapter()
   {
   }
@@ -154,8 +155,8 @@ public class AppletFormatAdapter
         String structureParser = StructureImportSettings
                 .getDefaultPDBFileParser();
         boolean isParseWithJMOL = structureParser.equalsIgnoreCase(
-                        StructureImportSettings.StructureParser.JMOL_PARSER
-                                .toString());
+                StructureImportSettings.StructureParser.JMOL_PARSER
+                        .toString());
         StructureImportSettings.addSettings(annotFromStructure,
                 localSecondaryStruct, serviceSecondaryStruct);
         if (isParseWithJMOL)
@@ -170,21 +171,20 @@ public class AppletFormatAdapter
                   localSecondaryStruct, serviceSecondaryStruct, inFile,
                   sourceType);
         }
-        ((StructureFile) alignFile).setDbRefType(FileFormat.PDB
-                .equals(fileFormat) ? Type.PDB : Type.MMCIF);
+        ((StructureFile) alignFile).setDbRefType(
+                FileFormat.PDB.equals(fileFormat) ? Type.PDB : Type.MMCIF);
       }
       else
       {
         // alignFile = fileFormat.getAlignmentFile(inFile, sourceType);
-        alignFile = fileFormat.getReader(new FileParse(inFile,
-                sourceType));
+        alignFile = fileFormat.getReader(new FileParse(inFile, sourceType));
       }
       return buildAlignmentFromFile();
     } catch (Exception e)
     {
       e.printStackTrace();
-      System.err.println("Failed to read alignment using the '"
-              + fileFormat + "' reader.\n" + e);
+      System.err.println("Failed to read alignment using the '" + fileFormat
+              + "' reader.\n" + e);
 
       if (e.getMessage() != null
               && e.getMessage().startsWith(INVALID_CHARACTERS))
@@ -333,10 +333,10 @@ public class AppletFormatAdapter
           AlignmentViewPanel ap, boolean selectedOnly)
   {
 
-    AlignmentView selvew = ap.getAlignViewport().getAlignmentView(
-            selectedOnly, false);
-    AlignmentI aselview = selvew.getVisibleAlignment(ap.getAlignViewport()
-            .getGapCharacter());
+    AlignmentView selvew = ap.getAlignViewport()
+            .getAlignmentView(selectedOnly, false);
+    AlignmentI aselview = selvew
+            .getVisibleAlignment(ap.getAlignViewport().getGapCharacter());
     List<AlignmentAnnotation> ala = (ap.getAlignViewport()
             .getVisibleAlignmentAnnotation(selectedOnly));
     if (ala != null)
@@ -399,8 +399,7 @@ public class AppletFormatAdapter
     } catch (Exception e)
     {
       System.err.println("Failed to write alignment as a '"
-              + format.getName()
-              + "' file\n");
+              + format.getName() + "' file\n");
       e.printStackTrace();
     }
 
@@ -446,10 +445,9 @@ public class AppletFormatAdapter
           System.gc();
           long memf = -r.totalMemory() + r.freeMemory();
           long t1 = -System.currentTimeMillis();
-          AlignmentI al = afa
-                  .readFile(args[i], DataSourceType.FILE,
-                          new IdentifyFile().identify(args[i],
-                                  DataSourceType.FILE));
+          AlignmentI al = afa.readFile(args[i], DataSourceType.FILE,
+                  new IdentifyFile().identify(args[i],
+                          DataSourceType.FILE));
           t1 += System.currentTimeMillis();
           System.gc();
           memf += r.totalMemory() - r.freeMemory();
@@ -459,12 +457,12 @@ public class AppletFormatAdapter
                     + " sequences and " + al.getWidth() + " columns.");
             try
             {
-              System.out.println(new AppletFormatAdapter().formatSequences(
-                      FileFormat.Fasta, al, true));
+              System.out.println(new AppletFormatAdapter()
+                      .formatSequences(FileFormat.Fasta, al, true));
             } catch (Exception e)
             {
-              System.err
-                      .println("Couln't format the alignment for output as a FASTA file.");
+              System.err.println(
+                      "Couln't format the alignment for output as a FASTA file.");
               e.printStackTrace(System.err);
             }
           }
@@ -473,8 +471,8 @@ public class AppletFormatAdapter
             System.out.println("Couldn't read alignment");
           }
           System.out.println("Read took " + (t1 / 1000.0) + " seconds.");
-          System.out
-                  .println("Difference between free memory now and before is "
+          System.out.println(
+                  "Difference between free memory now and before is "
                           + (memf / (1024.0 * 1024.0) * 1.0) + " MB");
         } catch (Exception e)
         {
@@ -558,8 +556,8 @@ public class AppletFormatAdapter
     {
       if (debug)
       {
-        System.out.println("Trying to get contents of resource as "
-                + protocol + ":");
+        System.out.println(
+                "Trying to get contents of resource as " + protocol + ":");
       }
       fp = new FileParse(file, protocol);
       if (!fp.isValid())