X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=da784208d9aceae920bc2fe9b3ff82c40db8afc5;hb=429bbdae3d5229ec1b92ec59f4b5a25bcfcf13f8;hp=1bb7ba3508269494d5e7869e799f8c9b4a34ac39;hpb=95ebbef7b78bf266a8252bd479510be3c80cd234;p=jalview.git

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 1bb7ba3..da78420 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;
 
@@ -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()
   {
   }
@@ -146,6 +147,20 @@ public class AppletFormatAdapter
   public AlignmentI readFile(String file, DataSourceType sourceType,
           FileFormatI fileFormat) throws IOException
   {
+    if (alignFile == null)
+    {
+      prepareFileReader(file, sourceType, fileFormat);
+    }
+    else
+    {
+      alignFile.parse();
+    }
+    return buildAlignmentFromFile();
+  }
+  
+  public void prepareFileReader(String file, DataSourceType sourceType,
+          FileFormatI fileFormat) throws IOException
+  {
     this.inFile = file;
     try
     {
@@ -154,8 +169,8 @@ 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 +185,19 @@ 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();
+      return;
     } 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))
@@ -200,7 +213,7 @@ public class AppletFormatAdapter
           // Possible sequence is just residues with no label
           alignFile = new FastaFile(">UNKNOWN\n" + inFile,
                   DataSourceType.PASTE);
-          return buildAlignmentFromFile();
+          return;
 
         } catch (Exception ex)
         {
@@ -333,10 +346,10 @@ 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)
@@ -370,7 +383,7 @@ public class AppletFormatAdapter
   {
     try
     {
-      AlignmentFileI afile = format.getWriter(alignment);
+      AlignmentFileWriterI afile = format.getWriter(alignment);
 
       afile.setNewlineString(newline);
       afile.setExportSettings(exportSettings);
@@ -399,23 +412,33 @@ 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();
     }
 
     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;
   }
 
@@ -435,10 +458,9 @@ 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();
@@ -448,12 +470,12 @@ 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);
             }
           }
@@ -462,8 +484,8 @@ 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)
         {
@@ -547,8 +569,8 @@ 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())
@@ -648,7 +670,7 @@ public class AppletFormatAdapter
     return null;
   }
 
-  public AlignmentFileI getAlignFile()
+  public AlignmentFileReaderI getAlignFile()
   {
     return alignFile;
   }