X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=c7b057578fbccdb3974aec814a330f0fe3ab9ba3;hb=9d8d94660cfba31f6dd39cd6a8a25e3e88284277;hp=1de01e6fd8f2e316d0357d91f56cdfd0d73036db;hpb=32a259190463ee06a81886db9d7843b565dea6df;p=jalview.git

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 1de01e6..c7b0575 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -1,233 +1,457 @@
-    /*
-    * Jalview - A Sequence Alignment Editor and Viewer
-    * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-    *
-    * This program 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 2
-    * of the License, or (at your option) any later version.
-    *
-    * This program 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 this program; if not, write to the Free Software
-    * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
-    */
-    package jalview.io;
-
-    import jalview.datamodel.*;
-
-    import java.util.Vector;
-
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @author $author$
-     * @version $Revision$
-     */
-    public class AppletFormatAdapter
-    {
-        /** DOCUMENT ME!! */
-        public static final String [] READABLE_FORMATS = new String[]
-        {
-            "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH", "PDB"
-        };
-
-        public static final String [] WRITEABLE_FORMATS = new String[]
-            {
-            "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM"
-        };
-
-
-        public static String INVALID_CHARACTERS = "Contains invalid characters";
-
-        public static String SUPPORTED_FORMATS = "Formats currently supported are\n" +
-                                                 "Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM";
-
-
-        public static String FILE = "File";
-        public static String URL = "URL";
-        public static String PASTE = "Paste";
-        public static String CLASSLOADER = "ClassLoader";
-
-
-        AlignFile afile = null;
-        String inFile;
-
-        public static final boolean isValidFormat(String format)
-        {
-          boolean valid = false;
-          for(int i=0; i<READABLE_FORMATS.length; i++)
-            if(READABLE_FORMATS[i].equalsIgnoreCase(format))
-              return true;
-
-          return valid;
-        }
-
-        /**
-         * DOCUMENT ME!
-         *
-         * @param inFile DOCUMENT ME!
-         * @param type DOCUMENT ME!
-         * @param format DOCUMENT ME!
-         *
-         * @return DOCUMENT ME!
-         */
-        public SequenceI[] readFile(String inFile, String type, String format)
-            throws java.io.IOException
-        {
-            this.inFile = inFile;
-            try
-            {
-              if (format.equals("FASTA"))
-              {
-                afile = new FastaFile(inFile, type);
-              }
-              else if (format.equals("MSF"))
-              {
-                afile = new MSFfile(inFile, type);
-              }
-              else if (format.equals("PileUp"))
-              {
-                afile = new PileUpfile(inFile, type);
-              }
-              else if (format.equals("CLUSTAL"))
-              {
-                afile = new ClustalFile(inFile, type);
-              }
-              else if (format.equals("BLC"))
-              {
-                afile = new BLCFile(inFile, type);
-              }
-              else if (format.equals("PIR"))
-              {
-                afile = new PIRFile(inFile, type);
-              }
-              else if (format.equals("PFAM"))
-              {
-                afile = new PfamFile(inFile, type);
-              }
-              else if (format.equals("JnetFile"))
-              {
-                afile = new JPredFile(inFile, type);
-                ( (JPredFile) afile).removeNonSequences();
-              }
-              else if (format.equals("PDB"))
-              {
-                afile = new MCview.PDBfile(inFile, type);
-              }
-              else if (format.equals("STH"))
-              {
-                afile = new StockholmFile(inFile, type);
-              }
-
-
-              return afile.getSeqsAsArray();
-            }
-            catch (Exception e)
-            {
-              e.printStackTrace();
-              System.err.println("Failed to read alignment using the '" + format +
-                                 "' reader.\n"+e);
-
-              if(e.getMessage()!=null && e.getMessage().startsWith(INVALID_CHARACTERS))
-                throw new java.io.IOException(e.getMessage());
-
-              // Finally test if the user has pasted just the sequence, no id
-              if(type.equalsIgnoreCase("Paste"))
-              {
-                try{
-                  // Possible sequence is just residues with no label
-                  afile = new FastaFile(">UNKNOWN\n" + inFile, "Paste");
-                  return afile.getSeqsAsArray();
-                }
-                catch(Exception ex)
-                {
-                  if(ex.toString().startsWith(INVALID_CHARACTERS))
-                    throw new java.io.IOException(e.getMessage());
-
-                  ex.printStackTrace();
-                }
-              }
-
-              // If we get to this stage, the format was not supported
-              throw new java.io.IOException(SUPPORTED_FORMATS);
-            }
-        }
-
-
-        /**
-         * DOCUMENT ME!
-         *
-         * @param format DOCUMENT ME!
-         * @param seqs DOCUMENT ME!
-         *
-         * @return DOCUMENT ME!
-         */
-        public String formatSequences(String format,
-                                      Vector seqs,
-                                      boolean jvsuffix)
-        {
-            SequenceI[] s = new SequenceI[seqs.size()];
-
-            for (int i = 0; i < seqs.size(); i++)
-                s[i] = (SequenceI) seqs.elementAt(i);
-
-            try
-            {
-                AlignFile afile = null;
-
-                if (format.equalsIgnoreCase("FASTA"))
-                {
-                    afile = new FastaFile();
-                }
-                else if (format.equalsIgnoreCase("MSF"))
-                {
-                    afile = new MSFfile();
-                }
-                else if (format.equalsIgnoreCase("PileUp"))
-                {
-                    afile = new PileUpfile();
-                }
-                else if (format.equalsIgnoreCase("CLUSTAL"))
-                {
-                    afile = new ClustalFile();
-                }
-                else if (format.equalsIgnoreCase("BLC"))
-                {
-                    afile = new BLCFile();
-                }
-                else if (format.equalsIgnoreCase("PIR"))
-                {
-                    afile = new PIRFile();
-                }
-                else if (format.equalsIgnoreCase("PFAM"))
-                {
-                    afile = new PfamFile();
-                }
-                else if (format.equalsIgnoreCase("STH"))
-                {
-                  afile = new StockholmFile();
-                }
-
-
-                afile.addJVSuffix(jvsuffix);
-
-                afile.setSeqs(s);
-
-                return afile.print();
-            }
-            catch (Exception e)
-            {
-                System.err.println("Failed to write alignment as a '" + format +
-                    "' file\n");
-                e.printStackTrace();
-            }
-
-            return null;
-        }
-    }
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program 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 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program 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 this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.io;
+
+import java.io.File;
+
+import jalview.datamodel.*;
+
+/**
+ * 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
+{
+  /** 
+   * 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"
+  };
+  /**
+   * 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"
+  };
+  /**
+   * 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, fastq", "aln", "pfam", "msf", "pir", "blc","amsa","jar" };
+  /**
+   * 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", "Jalview" };
+
+  /**
+   * 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"
+    };
+  /**
+   * 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"
+    };
+        
+  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);
+  /**
+   * 
+   * @param els
+   * @return grammatically correct(ish) list consisting of els elements.
+   */
+  public static String prettyPrint(String[] els) {
+    StringBuffer list = new StringBuffer();
+    for (int i=0,iSize=els.length-1; i<iSize;i++)
+    {
+      list.append(els[i]);
+      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;
+  String inFile;
+  /**
+   * 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
+   */
+  public static final boolean isValidFormat(String format)
+  {
+    return isValidFormat(format, false);
+  }
+  /**
+   * validate format is valid for IO
+   * @param format a format string to be compared with either READABLE_FORMATS or WRITEABLE_FORMATS
+   * @param forwriting when true, format is checked for containment in WRITEABLE_FORMATS
+   * @return true if format is valid
+   */
+  public static final boolean isValidFormat(String format, boolean forwriting)
+  {
+    boolean valid = false;
+    String[] format_list = (forwriting) ? WRITEABLE_FORMATS : READABLE_FORMATS;
+    for (int i = 0; i < format_list.length; i++)
+    {
+      if (format_list[i].equalsIgnoreCase(format))
+      {
+        return true;
+      }
+    }
+
+    return valid;
+  }
+  
+  /**
+   * 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)
+      throws java.io.IOException
+  {
+    // TODO: generalise mapping between format string and io. class instances using Constructor.invoke reflection
+    this.inFile = inFile;
+    try
+    {
+      if (format.equals("FASTA"))
+      {
+        afile = new FastaFile(inFile, type);
+      }
+      else if (format.equals("MSF"))
+      {
+        afile = new MSFfile(inFile, type);
+      }
+      else if (format.equals("PileUp"))
+      {
+        afile = new PileUpfile(inFile, type);
+      }
+      else if (format.equals("CLUSTAL"))
+      {
+        afile = new ClustalFile(inFile, type);
+      }
+      else if (format.equals("BLC"))
+      {
+        afile = new BLCFile(inFile, type);
+      }
+      else if (format.equals("PIR"))
+      {
+        afile = new PIRFile(inFile, type);
+      }
+      else if (format.equals("PFAM"))
+      {
+        afile = new PfamFile(inFile, type);
+      }
+      else if (format.equals("JnetFile"))
+      {
+        afile = new JPredFile(inFile, type);
+        ( (JPredFile) afile).removeNonSequences();
+      }
+      else if (format.equals("PDB"))
+      {
+        afile = new MCview.PDBfile(inFile, type);
+      }
+      else if (format.equals("STH"))
+      {
+        afile = new StockholmFile(inFile, type);
+      }
+
+      Alignment al = new Alignment(afile.getSeqsAsArray());
+
+      afile.addAnnotations(al);
+
+      return al;
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
+      System.err.println("Failed to read alignment using the '" + format +
+                         "' reader.\n" + e);
+
+      if (e.getMessage() != null &&
+          e.getMessage().startsWith(INVALID_CHARACTERS))
+      {
+        throw new java.io.IOException(e.getMessage());
+      }
+
+      // Finally test if the user has pasted just the sequence, no id
+      if (type.equalsIgnoreCase("Paste"))
+      {
+        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);
+          return al;
+
+        }
+        catch (Exception ex)
+        {
+          if (ex.toString().startsWith(INVALID_CHARACTERS))
+          {
+            throw new java.io.IOException(e.getMessage());
+          }
+
+          ex.printStackTrace();
+        }
+      }
+
+      // If we get to this stage, the format was not supported
+      throw new java.io.IOException(SUPPORTED_FORMATS);
+    }
+  }
+  /**
+   * 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)
+      throws java.io.IOException
+  {
+    // TODO: generalise mapping between format string and io. class instances using Constructor.invoke reflection
+    // This is exactly the same as the readFile method except we substitute 'inFile, type' with 'source'
+    this.inFile = source.getInFile();
+    String type = source.type;
+    try
+    {
+      if (format.equals("FASTA"))
+      {
+        afile = new FastaFile(source);
+      }
+      else if (format.equals("MSF"))
+      {
+        afile = new MSFfile(source);
+      }
+      else if (format.equals("PileUp"))
+      {
+        afile = new PileUpfile(source);
+      }
+      else if (format.equals("CLUSTAL"))
+      {
+        afile = new ClustalFile(source);
+      }
+      else if (format.equals("BLC"))
+      {
+        afile = new BLCFile(source);
+      }
+      else if (format.equals("PIR"))
+      {
+        afile = new PIRFile(source);
+      }
+      else if (format.equals("PFAM"))
+      {
+        afile = new PfamFile(source);
+      }
+      else if (format.equals("JnetFile"))
+      {
+        afile = new JPredFile(source);
+        ( (JPredFile) afile).removeNonSequences();
+      }
+      else if (format.equals("PDB"))
+      {
+        afile = new MCview.PDBfile(source);
+      }
+      else if (format.equals("STH"))
+      {
+        afile = new StockholmFile(source);
+      }
+
+      Alignment al = new Alignment(afile.getSeqsAsArray());
+
+      afile.addAnnotations(al);
+
+      return al;
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
+      System.err.println("Failed to read alignment using the '" + format +
+                         "' reader.\n" + e);
+
+      if (e.getMessage() != null &&
+          e.getMessage().startsWith(INVALID_CHARACTERS))
+      {
+        throw new java.io.IOException(e.getMessage());
+      }
+
+      // Finally test if the user has pasted just the sequence, no id
+      if (type.equalsIgnoreCase("Paste"))
+      {
+        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);
+          return al;
+
+        }
+        catch (Exception ex)
+        {
+          if (ex.toString().startsWith(INVALID_CHARACTERS))
+          {
+            throw new java.io.IOException(e.getMessage());
+          }
+
+          ex.printStackTrace();
+        }
+      }
+
+      // If we get to this stage, the format was not supported
+      throw new java.io.IOException(SUPPORTED_FORMATS);
+    }
+  }
+  
+  /**
+   * Construct an output class for an alignment in a particular filetype
+   *
+   * @param format string name of alignment format 
+   * @param alignment the alignment to be written out
+   * @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,
+                                boolean jvsuffix)
+  {
+    try
+    {
+      AlignFile afile = null;
+
+      if (format.equalsIgnoreCase("FASTA"))
+      {
+        afile = new FastaFile();
+      }
+      else if (format.equalsIgnoreCase("MSF"))
+      {
+        afile = new MSFfile();
+      }
+      else if (format.equalsIgnoreCase("PileUp"))
+      {
+        afile = new PileUpfile();
+      }
+      else if (format.equalsIgnoreCase("CLUSTAL"))
+      {
+        afile = new ClustalFile();
+      }
+      else if (format.equalsIgnoreCase("BLC"))
+      {
+        afile = new BLCFile();
+      }
+      else if (format.equalsIgnoreCase("PIR"))
+      {
+        afile = new PIRFile();
+      }
+      else if (format.equalsIgnoreCase("PFAM"))
+      {
+        afile = new PfamFile();
+      }
+      else if (format.equalsIgnoreCase("STH"))
+      {
+        afile = new StockholmFile();
+      }
+      else if (format.equalsIgnoreCase("AMSA"))
+      {
+        afile = new AMSAFile(alignment);
+      } else {
+        throw new Exception("Implementation error: Unknown file format string");
+      }
+
+      afile.addJVSuffix(jvsuffix);
+
+      afile.setSeqs(alignment.getSequencesArray());
+
+      return afile.print();
+    }
+    catch (Exception e)
+    {
+      System.err.println("Failed to write alignment as a '" + format +
+                         "' file\n");
+      e.printStackTrace();
+    }
+
+    return null;
+  }
+  public static void main(String[] args)
+  {
+    int i=0;
+    while (i<args.length)
+    {
+      File f = new File(args[i]);
+      if (f.exists())
+      {
+        try {
+          System.out.println("Reading file: "+f);
+          AppletFormatAdapter afa = new AppletFormatAdapter();
+          Runtime r = Runtime.getRuntime();
+          System.gc();
+          long memf = -r.totalMemory()+r.freeMemory();
+          long t1 = -System.currentTimeMillis();
+          Alignment al = afa.readFile(args[i], FILE, new IdentifyFile().Identify(args[i], FILE));
+          t1 +=System.currentTimeMillis();
+          System.gc();
+          memf += r.totalMemory()-r.freeMemory();
+          if (al!=null)
+          {
+            System.out.println("Alignment contains "+al.getHeight()+" sequences and "+al.getWidth()+" columns.");
+          } else {
+            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 "+(memf/(1024.0*1024.0)*1.0)+" MB");
+          
+        } catch (Exception e)
+        {
+          System.err.println("Exception when dealing with "+i+"'th argument: "+args[i]+"\n"+e);
+        }
+      } else {
+          System.err.println("Ignoring argument '"+args[i]+"' ("+i+"'th)- not a readable file.");
+      }
+      i++;
+    }
+    
+  }
+}