X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=56e9fa10ada182f95b7bcbb45b4a0c8c39dbde43;hb=c932f0e85a8852824cdd8ce790af68682732c85c;hp=04d68e8455180024b192abffa5efedd3b2c58540;hpb=8b27085fa7fc5f2877e078421284c2636b85b8c6;p=jalview.git

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 04d68e8..56e9fa1 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -20,7 +20,13 @@
  */
 package jalview.io;
 
-import jalview.api.AlignExportSettingI;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.List;
+import java.util.Locale;
+
+import jalview.api.AlignExportSettingsI;
 import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
@@ -30,11 +36,7 @@ import jalview.datamodel.PDBEntry.Type;
 import jalview.datamodel.SequenceI;
 import jalview.ext.jmol.JmolParser;
 import jalview.structure.StructureImportSettings;
-
-import java.io.File;
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.List;
+import jalview.util.Platform;
 
 /**
  * A low level class for alignment and feature IO with alignment formatting
@@ -64,7 +66,7 @@ public class AppletFormatAdapter
    */
   boolean serviceSecondaryStruct = false;
 
-  private AlignmentFileI alignFile = null;
+  private AlignmentFileReaderI alignFile = null;
 
   String inFile;
 
@@ -73,63 +75,22 @@ public class AppletFormatAdapter
    */
   protected String newline = System.getProperty("line.separator");
 
-  private AlignExportSettingI exportSettings;
-
-  /**
-   * List of valid format strings used in the isValidFormat method
-   */
-  public static final String[] READABLE_FORMATS = new String[] { "BLC",
-      "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH", "PDB",
-      "JnetFile", "RNAML", "PHYLIP", "JSON",
-      IdentifyFile.FeaturesFile, "HTML", "mmCIF" };
-
-  /**
-   * List of readable format file extensions by application in order
-   * corresponding to READABLE_FNAMES
-   */
-  public static final String[] READABLE_EXTENSIONS = new String[] {
-      "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
-      "sto,stk", "xml,rnaml", "phy", "json",
-      ".gff2,gff3", "jar,jvp", "html", "cif" };
-
-  /**
-   * List of readable formats by application in order corresponding to
-   * READABLE_EXTENSIONS
-   */
-  public static final String[] READABLE_FNAMES = new String[] { "Fasta",
-      "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Stockholm", "RNAML",
-      "PHYLIP", "JSON", IdentifyFile.FeaturesFile,
-      "Jalview", HtmlFile.FILE_DESC, "mmCIF" };
+  private AlignExportSettingsI exportSettings;
 
-  /**
-   * List of valid format strings for use by callers of the formatSequences
-   * method
-   */
-  public static final String[] WRITEABLE_FORMATS = new String[] { "BLC",
-      "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "AMSA", "STH",
-      "PHYLIP", "JSON" };
+  private File selectedFile;
 
-  /**
-   * List of extensions corresponding to file format types in WRITABLE_FNAMES
-   * that are writable by the application.
-   */
-  public static final String[] WRITABLE_EXTENSIONS = new String[] {
-      "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
-      "sto,stk", "phy", "json", "jvp" };
+  public static String INVALID_CHARACTERS = "Contains invalid characters";
 
   /**
-   * List of writable formats by the application. Order must correspond with the
-   * WRITABLE_EXTENSIONS list of formats.
+   * Returns an error message with a list of supported readable file formats
+   * 
+   * @return
    */
-  public static final String[] WRITABLE_FNAMES = new String[] { "Fasta",
-      "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "STH",
-      "PHYLIP", "JSON", "Jalview" };
-
-  public static String INVALID_CHARACTERS = "Contains invalid characters";
-
-  // TODO: make these messages dynamic
-  public static String SUPPORTED_FORMATS = "Formats currently supported are\n"
-          + prettyPrint(READABLE_FORMATS);
+  public static String getSupportedFormats()
+  {
+    return "Formats currently supported are\n"
+            + prettyPrint(FileFormats.getInstance().getReadableFormats());
+  }
 
   public AppletFormatAdapter()
   {
@@ -141,26 +102,28 @@ public class AppletFormatAdapter
   }
 
   public AppletFormatAdapter(AlignmentViewPanel alignPanel,
-          AlignExportSettingI settings)
+          AlignExportSettingsI settings)
   {
     viewpanel = alignPanel;
     exportSettings = settings;
   }
 
   /**
-   *
-   * @param els
-   * @return grammatically correct(ish) list consisting of els elements.
+   * Formats a grammatically correct(ish) list consisting of the given objects
+   * 
+   * @param things
+   * @return
    */
-  public static String prettyPrint(String[] els)
+  public static String prettyPrint(List<? extends Object> things)
   {
     StringBuffer list = new StringBuffer();
-    for (int i = 0, iSize = els.length - 1; i < iSize; i++)
+    for (int i = 0, iSize = things.size() - 1; i < iSize; i++)
     {
-      list.append(els[i]);
+      list.append(things.get(i).toString());
       list.append(", ");
     }
-    list.append(" and " + els[els.length - 1] + ".");
+    // could i18n 'and' here
+    list.append(" and " + things.get(things.size() - 1).toString() + ".");
     return list.toString();
   }
 
@@ -188,64 +151,71 @@ public class AppletFormatAdapter
   public AlignmentI readFile(String file, DataSourceType sourceType,
           FileFormatI fileFormat) throws IOException
   {
-    this.inFile = file;
+    return readFile(null, file, sourceType, fileFormat);
+  }
+
+  public AlignmentI readFile(File selectedFile, String file,
+          DataSourceType sourceType, FileFormatI fileFormat)
+          throws IOException
+  {
+    return readFile(selectedFile, file, sourceType, fileFormat, null);
+  }
+
+  public AlignmentI readFile(File selectedFile, String file,
+          DataSourceType sourceType, FileFormatI fileFormat,
+          StructureImportSettings.TFType tempfacType) throws IOException
+  {
+
+    this.selectedFile = selectedFile;
+    this.inFile = selectedFile != null ? selectedFile.getPath() : file;
     try
     {
-      if (fileFormat == FileFormat.PDB || fileFormat == FileFormat.MMCif)
+      if (fileFormat.isStructureFile())
       {
-        // TODO obtain config value from preference settings.
-        // Set value to 'true' to test PDB processing with Jmol: JAL-1213
-        boolean isParseWithJMOL = StructureImportSettings
-                .getDefaultPDBFileParser().equalsIgnoreCase(
-                        StructureImportSettings.StructureParser.JMOL_PARSER
-                                .toString());
+        String structureParser = StructureImportSettings
+                .getDefaultPDBFileParser();
+        boolean isParseWithJMOL = structureParser.equalsIgnoreCase(
+                StructureImportSettings.StructureParser.JMOL_PARSER
+                        .toString());
+        StructureImportSettings.addSettings(annotFromStructure,
+                localSecondaryStruct, serviceSecondaryStruct);
+        if (tempfacType != null)
+        {
+          StructureImportSettings.setTemperatureFactorType(tempfacType);
+        }
         if (isParseWithJMOL)
         {
-          StructureImportSettings.addSettings(annotFromStructure,
-                  localSecondaryStruct, serviceSecondaryStruct);
-          alignFile = new JmolParser(annotFromStructure,
-                  localSecondaryStruct, serviceSecondaryStruct, inFile,
-                  sourceType);
+          // needs a File option
+          alignFile = new JmolParser(
+                  selectedFile == null ? inFile : selectedFile, sourceType,
+                  StructureImportSettings.getTemperatureFactorType());
         }
         else
         {
-          StructureImportSettings.addSettings(annotFromStructure,
-                  localSecondaryStruct, serviceSecondaryStruct);
+          // todo is mc_view parsing obsolete yet? JAL-2120
           StructureImportSettings.setShowSeqFeatures(true);
-          alignFile = new MCview.PDBfile(annotFromStructure,
+          alignFile = new mc_view.PDBfile(annotFromStructure,
                   localSecondaryStruct, serviceSecondaryStruct, inFile,
                   sourceType);
         }
-        ((StructureFile) alignFile)
-                .setDbRefType(fileFormat == FileFormat.PDB ? Type.PDB
-                        : Type.MMCIF);
+        ((StructureFile) alignFile).setDbRefType(
+                FileFormat.PDB.equals(fileFormat) ? Type.PDB : Type.MMCIF);
+      }
+      else if (selectedFile != null)
+      {
+        alignFile = fileFormat
+                .getReader(new FileParse(selectedFile, sourceType));
       }
       else
       {
-        alignFile = fileFormat.getAlignmentFile(inFile, sourceType);
+        // alignFile = fileFormat.getAlignmentFile(inFile, sourceType);
+        alignFile = fileFormat.getReader(new FileParse(inFile, sourceType));
       }
-        // new FastaFile(inFile, sourceType);
-        // new MSFfile(inFile, sourceType);
-        // new PileUpfile(inFile, sourceType);
-        // new ClustalFile(inFile, sourceType);
-        // new BLCFile(inFile, sourceType);
-        // new PIRFile(inFile, sourceType);
-        // new PfamFile(inFile, sourceType);
-        // alignFile = new JPredFile(inFile, sourceType);
-        // ((JPredFile) alignFile).removeNonSequences();
-        // new StockholmFile(inFile, sourceType);
-        // new SimpleBlastFile(inFile, sourceType);
-        // new PhylipFile(inFile, sourceType);
-        // new JSONFile(inFile, sourceType);
-        // new HtmlFile(inFile, sourceType);
-        // new RnamlFile(inFile, sourceType);
-//        alignFile = new FeaturesFile(true, inFile, sourceType);
       return buildAlignmentFromFile();
     } catch (Exception e)
     {
       e.printStackTrace();
-      System.err.println("Failed to read alignment using the '"
-              + fileFormat
+      jalview.bin.Console.errPrintln("Failed to read alignment using the '" + fileFormat
               + "' reader.\n" + e);
 
       if (e.getMessage() != null
@@ -274,12 +244,12 @@ public class AppletFormatAdapter
           ex.printStackTrace();
         }
       }
-      if (fileFormat == FileFormat.Html)
+      if (FileFormat.Html.equals(fileFormat))
       {
         throw new IOException(e.getMessage());
       }
     }
-    throw new FileFormatException(SUPPORTED_FORMATS);
+    throw new FileFormatException(getSupportedFormats());
   }
 
   /**
@@ -299,7 +269,7 @@ public class AppletFormatAdapter
     DataSourceType type = source.dataSourceType;
     try
     {
-      if (format == FileFormat.PDB || format == FileFormat.MMCif)
+      if (FileFormat.PDB.equals(format) || FileFormat.MMCif.equals(format))
       {
         // TODO obtain config value from preference settings
         boolean isParseWithJMOL = false;
@@ -307,20 +277,19 @@ public class AppletFormatAdapter
         {
           StructureImportSettings.addSettings(annotFromStructure,
                   localSecondaryStruct, serviceSecondaryStruct);
-          alignFile = new JmolParser(annotFromStructure,
-                  localSecondaryStruct, serviceSecondaryStruct, source);
+          alignFile = new JmolParser(source);
         }
         else
         {
           StructureImportSettings.setShowSeqFeatures(true);
-          alignFile = new MCview.PDBfile(annotFromStructure,
+          alignFile = new mc_view.PDBfile(annotFromStructure,
                   localSecondaryStruct, serviceSecondaryStruct, source);
         }
         ((StructureFile) alignFile).setDbRefType(Type.PDB);
       }
       else
       {
-        alignFile = format.getAlignmentFile(source);
+        alignFile = format.getReader(source);
       }
 
       return buildAlignmentFromFile();
@@ -328,7 +297,7 @@ public class AppletFormatAdapter
     } catch (Exception e)
     {
       e.printStackTrace();
-      System.err.println("Failed to read alignment using the '" + format
+      jalview.bin.Console.errPrintln("Failed to read alignment using the '" + format
               + "' reader.\n" + e);
 
       if (e.getMessage() != null
@@ -359,7 +328,7 @@ public class AppletFormatAdapter
       }
 
       // If we get to this stage, the format was not supported
-      throw new FileFormatException(SUPPORTED_FORMATS);
+      throw new FileFormatException(getSupportedFormats());
     }
   }
 
@@ -396,10 +365,10 @@ 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)
@@ -433,7 +402,7 @@ public class AppletFormatAdapter
   {
     try
     {
-      AlignmentFileI afile = format.getAlignmentFile();
+      AlignmentFileWriterI afile = format.getWriter(alignment);
 
       afile.setNewlineString(newline);
       afile.setExportSettings(exportSettings);
@@ -455,32 +424,60 @@ public class AppletFormatAdapter
       String afileresp = afile.print(seqs, jvsuffix);
       if (afile.hasWarningMessage())
       {
-        System.err.println("Warning raised when writing as " + format
+        jalview.bin.Console.errPrintln("Warning raised when writing as " + format
                 + " : " + afile.getWarningMessage());
       }
       return afileresp;
     } catch (Exception e)
     {
-      System.err.println("Failed to write alignment as a '" + format
-              + "' file\n");
+      jalview.bin.Console.errPrintln("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
+   * 
+   * BH 2018 allows File or String, and can return RELATIVE_URL
+   *
+   * @param dataObject
+   *          File or String
+   * @return the protocol for the input data
+   */
+  public static DataSourceType checkProtocol(Object dataObject)
   {
-    DataSourceType protocol = DataSourceType.FILE;
-    String ft = file.toLowerCase().trim();
+    if (dataObject instanceof File)
+    {
+      return DataSourceType.FILE;
+    }
+
+    String data = dataObject.toString();
+    DataSourceType protocol = DataSourceType.PASTE;
+    String ft = data.toLowerCase(Locale.ROOT).trim();
     if (ft.indexOf("http:") == 0 || ft.indexOf("https:") == 0
             || ft.indexOf("file:") == 0)
     {
       protocol = DataSourceType.URL;
     }
+    else if (Platform.isJS())
+    {
+      protocol = DataSourceType.RELATIVE_URL;
+    }
+    else if (new File(data).exists())
+    {
+      protocol = DataSourceType.FILE;
+    }
     return protocol;
   }
 
+  /**
+   * @param args
+   * @j2sIgnore
+   */
   public static void main(String[] args)
   {
     int i = 0;
@@ -491,51 +488,50 @@ public class AppletFormatAdapter
       {
         try
         {
-          System.out.println("Reading file: " + f);
+          jalview.bin.Console.outPrintln("Reading file: " + f);
           AppletFormatAdapter afa = new AppletFormatAdapter();
           Runtime r = Runtime.getRuntime();
           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();
           if (al != null)
           {
-            System.out.println("Alignment contains " + al.getHeight()
+            jalview.bin.Console.outPrintln("Alignment contains " + al.getHeight()
                     + " sequences and " + al.getWidth() + " columns.");
             try
             {
-              System.out.println(new AppletFormatAdapter().formatSequences(
-                      FileFormat.Fasta, al, true));
+              jalview.bin.Console.outPrintln(new AppletFormatAdapter()
+                      .formatSequences(FileFormat.Fasta, al, true));
             } catch (Exception e)
             {
-              System.err
-                      .println("Couln't format the alignment for output as a FASTA file.");
+              jalview.bin.Console.errPrintln(
+                      "Couln't format the alignment for output as a FASTA file.");
               e.printStackTrace(System.err);
             }
           }
           else
           {
-            System.out.println("Couldn't read alignment");
+            jalview.bin.Console.outPrintln("Couldn't read alignment");
           }
-          System.out.println("Read took " + (t1 / 1000.0) + " seconds.");
-          System.out
-                  .println("Difference between free memory now and before is "
+          jalview.bin.Console.outPrintln("Read took " + (t1 / 1000.0) + " seconds.");
+          jalview.bin.Console.outPrintln(
+                  "Difference between free memory now and before is "
                           + (memf / (1024.0 * 1024.0) * 1.0) + " MB");
         } catch (Exception e)
         {
-          System.err.println("Exception when dealing with " + i
+          jalview.bin.Console.errPrintln("Exception when dealing with " + i
                   + "'th argument: " + args[i] + "\n" + e);
         }
       }
       else
       {
-        System.err.println("Ignoring argument '" + args[i] + "' (" + i
+        jalview.bin.Console.errPrintln("Ignoring argument '" + args[i] + "' (" + i
                 + "'th)- not a readable file.");
       }
       i++;
@@ -563,7 +559,7 @@ public class AppletFormatAdapter
     DataSourceType protocol = null;
     if (debug)
     {
-      System.out.println("resolving datasource started with:\n>>file\n"
+      jalview.bin.Console.outPrintln("resolving datasource started with:\n>>file\n"
               + file + ">>endfile");
     }
 
@@ -581,7 +577,7 @@ public class AppletFormatAdapter
       }
       if (debug)
       {
-        System.err.println("Resource '" + file + "' was "
+        jalview.bin.Console.errPrintln("Resource '" + file + "' was "
                 + (rtn ? "" : "not") + " located by classloader.");
       }
       if (rtn)
@@ -609,8 +605,8 @@ public class AppletFormatAdapter
     {
       if (debug)
       {
-        System.out.println("Trying to get contents of resource as "
-                + protocol + ":");
+        jalview.bin.Console.outPrintln(
+                "Trying to get contents of resource as " + protocol + ":");
       }
       fp = new FileParse(file, protocol);
       if (!fp.isValid())
@@ -621,14 +617,14 @@ public class AppletFormatAdapter
       {
         if (debug)
         {
-          System.out.println("Successful.");
+          jalview.bin.Console.outPrintln("Successful.");
         }
       }
     } catch (Exception e)
     {
       if (debug)
       {
-        System.err.println("Exception when accessing content: " + e);
+        jalview.bin.Console.errPrintln("Exception when accessing content: " + e);
       }
       fp = null;
     }
@@ -636,7 +632,7 @@ public class AppletFormatAdapter
     {
       if (debug)
       {
-        System.out.println("Accessing as paste.");
+        jalview.bin.Console.outPrintln("Accessing as paste.");
       }
       protocol = DataSourceType.PASTE;
       fp = null;
@@ -649,7 +645,7 @@ public class AppletFormatAdapter
         }
       } catch (Exception e)
       {
-        System.err.println("Failed to access content as paste!");
+        jalview.bin.Console.errPrintln("Failed to access content as paste!");
         e.printStackTrace();
         fp = null;
       }
@@ -666,26 +662,25 @@ public class AppletFormatAdapter
     {
       try
       {
-        FileFormatI idformat = new IdentifyFile().identify(file,
-                protocol);
+        FileFormatI idformat = new IdentifyFile().identify(file, protocol);
         if (idformat == null)
         {
           if (debug)
           {
-            System.out.println("Format not identified. Inaccessible file.");
+            jalview.bin.Console.outPrintln("Format not identified. Inaccessible file.");
           }
           return null;
         }
         if (debug)
         {
-          System.out.println("Format identified as " + idformat
+          jalview.bin.Console.outPrintln("Format identified as " + idformat
                   + "and expected as " + format);
         }
         if (idformat.equals(format))
         {
           if (debug)
           {
-            System.out.println("Protocol identified as " + protocol);
+            jalview.bin.Console.outPrintln("Protocol identified as " + protocol);
           }
           return protocol;
         }
@@ -703,7 +698,7 @@ public class AppletFormatAdapter
       {
         if (debug)
         {
-          System.err.println("File deemed not accessible via " + protocol);
+          jalview.bin.Console.errPrintln("File deemed not accessible via " + protocol);
           e.printStackTrace();
         }
       }
@@ -711,7 +706,7 @@ public class AppletFormatAdapter
     return null;
   }
 
-  public AlignmentFileI getAlignFile()
+  public AlignmentFileReaderI getAlignFile()
   {
     return alignFile;
   }