X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=de9e6bdd63d70f61249150f2a11f3376225845b9;hb=2a9991ef1eb02d97e9c8ed1644f292117ae6f600;hp=b1952a9fc66e060730fa6a936a09f5db844b1c62;hpb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;p=jalview.git

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index b1952a9..de9e6bd 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -1,87 +1,132 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- * 
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
  * This file is part of Jalview.
- * 
+ *
  * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
- * Jalview is distributed in the hope that it will be useful, but 
- * WITHOUT ANY WARRANTY; without even the implied warranty 
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  * PURPOSE.  See the GNU General Public License for more details.
- * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.io;
 
 import java.io.File;
 import java.io.InputStream;
+import java.util.List;
 
-import jalview.datamodel.*;
+import jalview.api.AlignViewportI;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.SequenceGroup;
+import jalview.util.MessageManager;
 
 /**
  * A low level class for alignment and feature IO with alignment formatting
  * methods used by both applet and application for generating flat alignment
  * files. It also holds the lists of magic format names that the applet and
  * application will allow the user to read or write files with.
- * 
+ *
  * @author $author$
  * @version $Revision$
  */
 public class AppletFormatAdapter
 {
+  private AlignViewportI viewport;
+
+  public static String FILE = "File";
+
+  public static String URL = "URL";
+
+  public static String PASTE = "Paste";
+
+  public static String CLASSLOADER = "ClassLoader";
+
   /**
-   * List of valid format strings used in the isValidFormat method
+   * add jalview-derived non-secondary structure annotation from PDB structure
    */
-  public static final String[] READABLE_FORMATS = new String[]
-  { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH",
-      "PDB", "JnetFile" }; // , "SimpleBLAST" };
+  boolean annotFromStructure = false;
 
   /**
-   * List of valid format strings for use by callers of the formatSequences
-   * method
+   * add secondary structure from PDB data with built-in algorithms
    */
-  public static final String[] WRITEABLE_FORMATS = new String[]
-  { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "AMSA" };
+  boolean localSecondaryStruct = false;
 
   /**
-   * List of extensions corresponding to file format types in WRITABLE_FNAMES
-   * that are writable by the application.
+   * process PDB data with web services
    */
-  public static final String[] WRITABLE_EXTENSIONS = new String[]
-  { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar" };
+  boolean serviceSecondaryStruct = false;
+
+  private AlignFile alignFile = null;
+
+  String inFile;
 
   /**
-   * List of writable formats by the application. Order must correspond with the
-   * WRITABLE_EXTENSIONS list of formats.
+   * character used to write newlines
    */
-  public static final String[] WRITABLE_FNAMES = new String[]
-  { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview" };
+  protected String newline = System.getProperty("line.separator");
+
+  /**
+   * 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", PhylipFile.FILE_DESC, JSONFile.FILE_DESC, IdentifyFile.GFF3File,
+      "HTML" };
 
   /**
    * List of readable format file extensions by application in order
    * corresponding to READABLE_FNAMES
    */
   public static final String[] READABLE_EXTENSIONS = new String[]
-  { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
-      "sto" }; // ,
-
-  // ".blast"
-  // };
+  { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
+      "sto,stk", "xml,rnaml", PhylipFile.FILE_EXT, JSONFile.FILE_EXT,
+      ".gff2,gff3",
+      "jar,jvp", HtmlFile.FILE_EXT };
 
   /**
    * 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", "Jalview",
-      "Stockholm" };// ,
+  { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Stockholm",
+      "RNAML", PhylipFile.FILE_DESC, JSONFile.FILE_DESC, IdentifyFile.GFF3File, "Jalview",
+      HtmlFile.FILE_DESC };
+
+  /**
+   * 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", PhylipFile.FILE_DESC, JSONFile.FILE_DESC };
 
-  // "SimpleBLAST"
-  // };
+  /**
+   * 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", PhylipFile.FILE_EXT, JSONFile.FILE_EXT, "jvp" };
+
+  /**
+   * List of writable formats by the application. Order must correspond with the
+   * WRITABLE_EXTENSIONS list of formats.
+   */
+  public static final String[] WRITABLE_FNAMES = new String[]
+  { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "STH",
+      PhylipFile.FILE_DESC, JSONFile.FILE_DESC, "Jalview" };
 
   public static String INVALID_CHARACTERS = "Contains invalid characters";
 
@@ -89,8 +134,17 @@ public class AppletFormatAdapter
   public static String SUPPORTED_FORMATS = "Formats currently supported are\n"
           + prettyPrint(READABLE_FORMATS);
 
+  public AppletFormatAdapter()
+  {
+  }
+
+  public AppletFormatAdapter(AlignViewportI viewport)
+  {
+    this.viewport = viewport;
+  }
+
   /**
-   * 
+   *
    * @param els
    * @return grammatically correct(ish) list consisting of els elements.
    */
@@ -100,27 +154,26 @@ public class AppletFormatAdapter
     for (int i = 0, iSize = els.length - 1; i < iSize; i++)
     {
       list.append(els[i]);
-      list.append(",");
+      list.append(", ");
     }
     list.append(" and " + els[els.length - 1] + ".");
     return list.toString();
   }
 
-  public static String FILE = "File";
 
-  public static String URL = "URL";
-
-  public static String PASTE = "Paste";
-
-  public static String CLASSLOADER = "ClassLoader";
-
-  AlignFile afile = null;
+  public void setNewlineString(String nl)
+  {
+    newline = nl;
+  }
 
-  String inFile;
+  public String getNewlineString()
+  {
+    return newline;
+  }
 
   /**
    * check that this format is valid for reading
-   * 
+   *
    * @param format
    *          a format string to be compared with READABLE_FORMATS
    * @return true if format is readable
@@ -132,7 +185,7 @@ public class AppletFormatAdapter
 
   /**
    * validate format is valid for IO
-   * 
+   *
    * @param format
    *          a format string to be compared with either READABLE_FORMATS or
    *          WRITEABLE_FORMATS
@@ -146,9 +199,9 @@ public class AppletFormatAdapter
     boolean valid = false;
     String[] format_list = (forwriting) ? WRITEABLE_FORMATS
             : READABLE_FORMATS;
-    for (int i = 0; i < format_list.length; i++)
+    for (String element : format_list)
     {
-      if (format_list[i].equalsIgnoreCase(format))
+      if (element.equalsIgnoreCase(format))
       {
         return true;
       }
@@ -159,14 +212,14 @@ public class AppletFormatAdapter
 
   /**
    * Constructs the correct filetype parser for a characterised datasource
-   * 
+   *
    * @param inFile
    *          data/data location
    * @param type
    *          type of datasource
    * @param format
    *          File format of data provided by datasource
-   * 
+   *
    * @return DOCUMENT ME!
    */
   public Alignment readFile(String inFile, String type, String format)
@@ -177,55 +230,95 @@ public class AppletFormatAdapter
     this.inFile = inFile;
     try
     {
+      Alignment al;
       if (format.equals("FASTA"))
       {
-        afile = new FastaFile(inFile, type);
+        alignFile = new FastaFile(inFile, type);
       }
       else if (format.equals("MSF"))
       {
-        afile = new MSFfile(inFile, type);
+        alignFile = new MSFfile(inFile, type);
       }
       else if (format.equals("PileUp"))
       {
-        afile = new PileUpfile(inFile, type);
+        alignFile = new PileUpfile(inFile, type);
       }
       else if (format.equals("CLUSTAL"))
       {
-        afile = new ClustalFile(inFile, type);
+        alignFile = new ClustalFile(inFile, type);
       }
       else if (format.equals("BLC"))
       {
-        afile = new BLCFile(inFile, type);
+        alignFile = new BLCFile(inFile, type);
       }
       else if (format.equals("PIR"))
       {
-        afile = new PIRFile(inFile, type);
+        alignFile = new PIRFile(inFile, type);
       }
       else if (format.equals("PFAM"))
       {
-        afile = new PfamFile(inFile, type);
+        alignFile = new PfamFile(inFile, type);
       }
       else if (format.equals("JnetFile"))
       {
-        afile = new JPredFile(inFile, type);
-        ((JPredFile) afile).removeNonSequences();
+        alignFile = new JPredFile(inFile, type);
+        ((JPredFile) alignFile).removeNonSequences();
       }
       else if (format.equals("PDB"))
       {
-        afile = new MCview.PDBfile(inFile, type);
+        alignFile = new MCview.PDBfile(annotFromStructure,
+                localSecondaryStruct, serviceSecondaryStruct, inFile, type);
+        // Uncomment to test Jmol data based PDB processing: JAL-1213
+        // afile = new jalview.ext.jmol.PDBFileWithJmol(inFile, type);
       }
       else if (format.equals("STH"))
       {
-        afile = new StockholmFile(inFile, type);
+        alignFile = new StockholmFile(inFile, type);
       }
       else if (format.equals("SimpleBLAST"))
       {
-        afile = new SimpleBlastFile(inFile, type);
+        alignFile = new SimpleBlastFile(inFile, type);
+      }
+      else if (format.equals(PhylipFile.FILE_DESC))
+      {
+        alignFile = new PhylipFile(inFile, type);
       }
+      else if (format.equals(JSONFile.FILE_DESC))
+      {
+        alignFile = new JSONFile(inFile, type);
+        al = new Alignment(alignFile.getSeqsAsArray());
+        alignFile.addAnnotations(al);
+        ((JSONFile) alignFile).setViewport(viewport);
+        for (SequenceGroup sg : alignFile.getSeqGroups())
+        {
+          al.addGroup(sg);
+        }
 
-      Alignment al = new Alignment(afile.getSeqsAsArray());
+        return al;
+      }
+      else if (format.equals(HtmlFile.FILE_DESC))
+      {
+        alignFile = new HtmlFile(inFile, type);
+        al = new Alignment(alignFile.getSeqsAsArray());
+        alignFile.addAnnotations(al);
+        for (SequenceGroup sg : alignFile.getSeqGroups())
+        {
+          al.addGroup(sg);
+        }
+        return al;
+      }
+      else if (format.equals("RNAML"))
+      {
+        alignFile = new RnamlFile(inFile, type);
+      }
+      else if (format.equals(IdentifyFile.GFF3File))
+      {
+        alignFile = new Gff3File(inFile, type);
+      }
+
+      al = new Alignment(alignFile.getSeqsAsArray());
 
-      afile.addAnnotations(al);
+      alignFile.addAnnotations(al);
 
       return al;
     } catch (Exception e)
@@ -246,9 +339,11 @@ public class AppletFormatAdapter
         try
         {
           // Possible sequence is just residues with no label
-          afile = new FastaFile(">UNKNOWN\n" + inFile, "Paste");
-          Alignment al = new Alignment(afile.getSeqsAsArray());
-          afile.addAnnotations(al);
+          alignFile = new FastaFile(">UNKNOWN\n" + inFile, "Paste");
+          Alignment al = new Alignment(alignFile.getSeqsAsArray());
+
+          alignFile.addSeqGroups(al);
+          alignFile.addAnnotations(al);
           return al;
 
         } catch (Exception ex)
@@ -269,15 +364,15 @@ public class AppletFormatAdapter
 
   /**
    * Constructs the correct filetype parser for an already open datasource
-   * 
+   *
    * @param source
    *          an existing datasource
    * @param format
    *          File format of data that will be provided by datasource
-   * 
+   *
    * @return DOCUMENT ME!
    */
-  public Alignment readFromFile(FileParse source, String format)
+  public AlignmentI readFromFile(FileParse source, String format)
           throws java.io.IOException
   {
     // TODO: generalise mapping between format string and io. class instances
@@ -288,55 +383,79 @@ public class AppletFormatAdapter
     String type = source.type;
     try
     {
+      Alignment al;
       if (format.equals("FASTA"))
       {
-        afile = new FastaFile(source);
+        alignFile = new FastaFile(source);
       }
       else if (format.equals("MSF"))
       {
-        afile = new MSFfile(source);
+        alignFile = new MSFfile(source);
       }
       else if (format.equals("PileUp"))
       {
-        afile = new PileUpfile(source);
+        alignFile = new PileUpfile(source);
       }
       else if (format.equals("CLUSTAL"))
       {
-        afile = new ClustalFile(source);
+        alignFile = new ClustalFile(source);
       }
       else if (format.equals("BLC"))
       {
-        afile = new BLCFile(source);
+        alignFile = new BLCFile(source);
       }
       else if (format.equals("PIR"))
       {
-        afile = new PIRFile(source);
+        alignFile = new PIRFile(source);
       }
       else if (format.equals("PFAM"))
       {
-        afile = new PfamFile(source);
+        alignFile = new PfamFile(source);
       }
       else if (format.equals("JnetFile"))
       {
-        afile = new JPredFile(source);
-        ((JPredFile) afile).removeNonSequences();
+        alignFile = new JPredFile(source);
+        ((JPredFile) alignFile).removeNonSequences();
       }
       else if (format.equals("PDB"))
       {
-        afile = new MCview.PDBfile(source);
+        alignFile = new MCview.PDBfile(annotFromStructure,
+                localSecondaryStruct, serviceSecondaryStruct, source);
       }
       else if (format.equals("STH"))
       {
-        afile = new StockholmFile(source);
+        alignFile = new StockholmFile(source);
+      }
+      else if (format.equals("RNAML"))
+      {
+        alignFile = new RnamlFile(source);
       }
       else if (format.equals("SimpleBLAST"))
       {
-        afile = new SimpleBlastFile(source);
+        alignFile = new SimpleBlastFile(source);
       }
-
-      Alignment al = new Alignment(afile.getSeqsAsArray());
-
-      afile.addAnnotations(al);
+      else if (format.equals(PhylipFile.FILE_DESC))
+      {
+        alignFile = new PhylipFile(source);
+      }
+      else if (format.equals(IdentifyFile.GFF3File))
+      {
+        alignFile = new Gff3File(inFile, type);
+      }
+      else if (format.equals(JSONFile.FILE_DESC))
+      {
+        alignFile = new JSONFile(source);
+        al = new Alignment(alignFile.getSeqsAsArray());
+        alignFile.addAnnotations(al);
+        alignFile.addSeqGroups(al);
+        return al;
+      }
+      else if (format.equals(HtmlFile.FILE_DESC))
+      {
+        alignFile = new HtmlFile(source);
+      }
+      al = new Alignment(alignFile.getSeqsAsArray());
+      alignFile.addAnnotations(al);
 
       return al;
     } catch (Exception e)
@@ -357,9 +476,10 @@ public class AppletFormatAdapter
         try
         {
           // Possible sequence is just residues with no label
-          afile = new FastaFile(">UNKNOWN\n" + inFile, "Paste");
-          Alignment al = new Alignment(afile.getSeqsAsArray());
-          afile.addAnnotations(al);
+          alignFile = new FastaFile(">UNKNOWN\n" + inFile, "Paste");
+          Alignment al = new Alignment(alignFile.getSeqsAsArray());
+          alignFile.addAnnotations(al);
+          alignFile.addSeqGroups(al);
           return al;
 
         } catch (Exception ex)
@@ -378,11 +498,40 @@ public class AppletFormatAdapter
     }
   }
 
+
+  /**
+   * create an alignment flatfile from a Jalview alignment view
+   * @param format
+   * @param jvsuffix
+   * @param av
+   * @param selectedOnly
+   * @return flatfile in a string
+   */
+  public String formatSequences(String format, boolean jvsuffix,
+          AlignViewportI av, boolean selectedOnly)
+  {
+
+    AlignmentView selvew = av.getAlignmentView(selectedOnly, false);
+    AlignmentI aselview = selvew.getVisibleAlignment(av
+            .getGapCharacter());
+    List<AlignmentAnnotation> ala = (av
+            .getVisibleAlignmentAnnotation(selectedOnly));
+    if (ala != null)
+    {
+      for (AlignmentAnnotation aa : ala)
+      {
+        aselview.addAnnotation(aa);
+      }
+    }
+
+    return formatSequences(format, aselview, jvsuffix);
+  }
+
   /**
    * Construct an output class for an alignment in a particular filetype TODO:
    * allow caller to detect errors and warnings encountered when generating
    * output
-   * 
+   *
    * @param format
    *          string name of alignment format
    * @param alignment
@@ -390,7 +539,7 @@ public class AppletFormatAdapter
    * @param jvsuffix
    *          passed to AlnFile class controls whether /START-END is added to
    *          sequence names
-   * 
+   *
    * @return alignment flat file contents
    */
   public String formatSequences(String format, AlignmentI alignment,
@@ -399,7 +548,6 @@ public class AppletFormatAdapter
     try
     {
       AlignFile afile = null;
-
       if (format.equalsIgnoreCase("FASTA"))
       {
         afile = new FastaFile();
@@ -430,22 +578,51 @@ public class AppletFormatAdapter
       }
       else if (format.equalsIgnoreCase("STH"))
       {
-        afile = new StockholmFile();
+        afile = new StockholmFile(alignment);
       }
       else if (format.equalsIgnoreCase("AMSA"))
       {
         afile = new AMSAFile(alignment);
       }
-      else
+      else if (format.equalsIgnoreCase(PhylipFile.FILE_DESC))
+      {
+        afile = new PhylipFile();
+      }
+       else if (format.equalsIgnoreCase(JSONFile.FILE_DESC))
+       {
+        afile = new JSONFile();
+        afile.setViewport(viewport);
+        // Add groups to AlignFile
+        afile.seqGroups = alignment.getGroups();
+
+        // Add non auto calculated annotation to AlignFile
+        for (AlignmentAnnotation annot : alignment.getAlignmentAnnotation())
+        {
+          if (annot != null && !annot.autoCalculated)
+          {
+            if (annot.label.equals("PDB.CATempFactor"))
+            {
+              continue;
+            }
+            afile.annotations.add(annot);
+          }
+        }
+       }
+      else if (format.equalsIgnoreCase("RNAML"))
       {
-        throw new Exception(
-                "Implementation error: Unknown file format string");
+        afile = new RnamlFile();
       }
 
+      else
+      {
+        throw new Exception(MessageManager.getString("error.implementation_error_unknown_file_format_string"));
+      }
+      afile.setNewlineString(newline);
       afile.addJVSuffix(jvsuffix);
 
       afile.setSeqs(alignment.getSequencesArray());
 
+
       String afileresp = afile.print();
       if (afile.hasWarningMessage())
       {
@@ -463,6 +640,18 @@ public class AppletFormatAdapter
     return null;
   }
 
+  public static String checkProtocol(String file)
+  {
+    String protocol = FILE;
+    String ft = file.toLowerCase().trim();
+    if (ft.indexOf("http:") == 0 || ft.indexOf("https:") == 0
+            || ft.indexOf("file:") == 0)
+    {
+      protocol = URL;
+    }
+    return protocol;
+  }
+
   public static void main(String[] args)
   {
     int i = 0;
@@ -495,7 +684,7 @@ public class AppletFormatAdapter
             } catch (Exception e)
             {
               System.err
-                      .println("Couln't format the alignment for output as a FASTA file.");
+              .println("Couln't format the alignment for output as a FASTA file.");
               e.printStackTrace(System.err);
             }
           }
@@ -505,9 +694,8 @@ public class AppletFormatAdapter
           }
           System.out.println("Read took " + (t1 / 1000.0) + " seconds.");
           System.out
-                  .println("Difference between free memory now and before is "
-                          + (memf / (1024.0 * 1024.0) * 1.0) + " MB");
-
+          .println("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
@@ -526,7 +714,7 @@ public class AppletFormatAdapter
   /**
    * try to discover how to access the given file as a valid datasource that
    * will be identified as the given type.
-   * 
+   *
    * @param file
    * @param format
    * @return protocol that yields the data parsable as the given type
@@ -573,7 +761,7 @@ public class AppletFormatAdapter
     } catch (Exception ex)
     {
       System.err
-              .println("Exception checking resources: " + file + " " + ex);
+      .println("Exception checking resources: " + file + " " + ex);
     }
 
     if (file.indexOf("://") > -1)
@@ -675,7 +863,7 @@ public class AppletFormatAdapter
           if (debug)
           {
             System.out
-                    .println("File deemed not accessible via " + protocol);
+            .println("File deemed not accessible via " + protocol);
           }
           fp.close();
           return null;
@@ -693,4 +881,14 @@ public class AppletFormatAdapter
     }
     return null;
   }
+
+  public AlignFile getAlignFile()
+  {
+    return alignFile;
+  }
+
+  public void setAlignFile(AlignFile alignFile)
+  {
+    this.alignFile = alignFile;
+  }
 }