X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;fp=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=5e209e6569970c260d95410ebd1c853e4b0a37b0;hb=f063821ed0be9c1581af74643a1aa5798731af65;hp=45d65d61065ddaef9c6f32f21cabbf1ca8d7ca57;hpb=fd18e2c73cd015d4e38ad91da0e5d7532ff0ef42;p=jalview.git

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 45d65d6..5e209e6 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -64,7 +64,7 @@ public class AppletFormatAdapter
    */
   boolean serviceSecondaryStruct = false;
 
-  private AlignmentFileI alignFile = null;
+  private AlignmentFileReaderI alignFile = null;
 
   String inFile;
 
@@ -77,8 +77,16 @@ public class AppletFormatAdapter
 
   public static String INVALID_CHARACTERS = "Contains invalid characters";
 
-  public static String SUPPORTED_FORMATS = "Formats currently supported are\n"
-          + prettyPrint(FileFormat.getReadableFormats());
+  /**
+   * Returns an error message with a list of supported readable file formats
+   * 
+   * @return
+   */
+  public static String getSupportedFormats()
+  {
+    return "Formats currently supported are\n"
+            + prettyPrint(FileFormats.getInstance().getReadableFormats());
+  }
 
   public AppletFormatAdapter()
   {
@@ -147,8 +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)
@@ -157,25 +165,26 @@ public class AppletFormatAdapter
         }
         else
         {
-          // todo is MCview parsing obsolete yet?
+          // todo is MCview parsing obsolete yet? JAL-2120
           StructureImportSettings.setShowSeqFeatures(true);
           alignFile = new MCview.PDBfile(annotFromStructure,
                   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.getAlignmentFile(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))
@@ -208,7 +217,7 @@ public class AppletFormatAdapter
         throw new IOException(e.getMessage());
       }
     }
-    throw new FileFormatException(SUPPORTED_FORMATS);
+    throw new FileFormatException(getSupportedFormats());
   }
 
   /**
@@ -248,7 +257,7 @@ public class AppletFormatAdapter
       }
       else
       {
-        alignFile = format.getAlignmentFile(source);
+        alignFile = format.getReader(source);
       }
 
       return buildAlignmentFromFile();
@@ -287,7 +296,7 @@ public class AppletFormatAdapter
       }
 
       // If we get to this stage, the format was not supported
-      throw new FileFormatException(SUPPORTED_FORMATS);
+      throw new FileFormatException(getSupportedFormats());
     }
   }
 
@@ -324,10 +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)
@@ -361,7 +370,7 @@ public class AppletFormatAdapter
   {
     try
     {
-      AlignmentFileI afile = format.getAlignmentFile(alignment);
+      AlignmentFileWriterI afile = format.getWriter(alignment);
 
       afile.setNewlineString(newline);
       afile.setExportSettings(exportSettings);
@@ -389,23 +398,34 @@ public class AppletFormatAdapter
       return afileresp;
     } catch (Exception e)
     {
-      System.err.println("Failed to write alignment as a '" + format
-              + "' file\n");
+      System.err.println("Failed to write alignment as a '"
+              + format.getName() + "' file\n");
       e.printStackTrace();
     }
 
     return null;
   }
 
-  public static DataSourceType checkProtocol(String file)
+  /**
+   * Determines the protocol (i.e DataSourceType.{FILE|PASTE|URL}) for the input
+   * data
+   *
+   * @param data
+   * @return the protocol for the input data
+   */
+  public static DataSourceType checkProtocol(String data)
   {
-    DataSourceType protocol = DataSourceType.FILE;
-    String ft = file.toLowerCase().trim();
+    DataSourceType protocol = DataSourceType.PASTE;
+    String ft = data.toLowerCase().trim();
     if (ft.indexOf("http:") == 0 || ft.indexOf("https:") == 0
             || ft.indexOf("file:") == 0)
     {
       protocol = DataSourceType.URL;
     }
+    else if (new File(data).exists())
+    {
+      protocol = DataSourceType.FILE;
+    }
     return protocol;
   }
 
@@ -425,10 +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();
@@ -438,12 +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);
             }
           }
@@ -452,8 +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)
         {
@@ -537,8 +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())
@@ -638,7 +657,7 @@ public class AppletFormatAdapter
     return null;
   }
 
-  public AlignmentFileI getAlignFile()
+  public AlignmentFileReaderI getAlignFile()
   {
     return alignFile;
   }