X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=ee242386383f0233c473181525308eecaef645ec;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=fbfaab131fba87b73e372fff2d5513f1b4676697;hpb=7cb5308c5ec411a566d131993e63abaaf7f7c7b9;p=jalview.git

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index fbfaab1..ee24238 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -1,97 +1,154 @@
 /*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 
+ * 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 
+ * 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/>.
  */
 package jalview.io;
 
+import java.io.File;
+import java.io.InputStream;
+
 import jalview.datamodel.*;
 
 /**
- * DOCUMENT ME!
- *
+ * 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
 {
-  /** DOCUMENT ME!! */
+  /**
+   * 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"
-  };
+  { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH",
+      "PDB", "JnetFile" }; // , "SimpleBLAST" };
 
+  /**
+   * 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"
-  };
+  { "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" };
+  { "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" };
+  { "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",
+      "sto" }; // ,
+
+  // ".blast"
+  // };
+
+  /**
+   * 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" };// ,
+
+  // "SimpleBLAST"
+  // };
 
-  public static final String[] READABLE_EXTENSIONS =         new String[]
-        {
-        "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
-        "amsa","jar"
-    };
-  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);
+  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) {
+  public static String prettyPrint(String[] els)
+  {
     StringBuffer list = new StringBuffer();
-    for (int i=0,iSize=els.length-1; i<iSize;i++)
+    for (int i = 0, iSize = els.length - 1; i < iSize; i++)
     {
       list.append(els[i]);
       list.append(",");
     }
-    list.append(" and "+els[els.length-1]+".");
+    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
+   * 
+   * @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;
-    for (int i = 0; i < READABLE_FORMATS.length; i++)
+    String[] format_list = (forwriting) ? WRITEABLE_FORMATS
+            : READABLE_FORMATS;
+    for (int i = 0; i < format_list.length; i++)
     {
-      if (READABLE_FORMATS[i].equalsIgnoreCase(format))
+      if (format_list[i].equalsIgnoreCase(format))
       {
         return true;
       }
@@ -102,16 +159,21 @@ 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
-   *
+   * 
+   * @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
+          throws java.io.IOException
   {
+    // TODO: generalise mapping between format string and io. class instances
+    // using Constructor.invoke reflection
     this.inFile = inFile;
     try
     {
@@ -146,7 +208,7 @@ public class AppletFormatAdapter
       else if (format.equals("JnetFile"))
       {
         afile = new JPredFile(inFile, type);
-        ( (JPredFile) afile).removeNonSequences();
+        ((JPredFile) afile).removeNonSequences();
       }
       else if (format.equals("PDB"))
       {
@@ -156,21 +218,24 @@ public class AppletFormatAdapter
       {
         afile = new StockholmFile(inFile, type);
       }
+      else if (format.equals("SimpleBLAST"))
+      {
+        afile = new SimpleBlastFile(inFile, type);
+      }
 
       Alignment al = new Alignment(afile.getSeqsAsArray());
 
       afile.addAnnotations(al);
 
       return al;
-    }
-    catch (Exception e)
+    } catch (Exception e)
     {
       e.printStackTrace();
-      System.err.println("Failed to read alignment using the '" + format +
-                         "' reader.\n" + e);
+      System.err.println("Failed to read alignment using the '" + format
+              + "' reader.\n" + e);
 
-      if (e.getMessage() != null &&
-          e.getMessage().startsWith(INVALID_CHARACTERS))
+      if (e.getMessage() != null
+              && e.getMessage().startsWith(INVALID_CHARACTERS))
       {
         throw new java.io.IOException(e.getMessage());
       }
@@ -186,8 +251,118 @@ public class AppletFormatAdapter
           afile.addAnnotations(al);
           return al;
 
+        } catch (Exception ex)
+        {
+          if (ex.toString().startsWith(INVALID_CHARACTERS))
+          {
+            throw new java.io.IOException(e.getMessage());
+          }
+
+          ex.printStackTrace();
         }
-        catch (Exception ex)
+      }
+
+      // 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);
+      }
+      else if (format.equals("SimpleBLAST"))
+      {
+        afile = new SimpleBlastFile(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))
           {
@@ -204,17 +379,22 @@ public class AppletFormatAdapter
   }
 
   /**
-   * Construct an output class for an alignment in a particular filetype
-   *
-   * @param format DOCUMENT ME!
-   * @param seqs DOCUMENT ME!
-   * @param jvsuffix passed to AlnFile class
-   *
+   * 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
+   *          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)
+  public String formatSequences(String format, AlignmentI alignment,
+          boolean jvsuffix)
   {
     try
     {
@@ -255,23 +435,259 @@ public class AppletFormatAdapter
       else if (format.equalsIgnoreCase("AMSA"))
       {
         afile = new AMSAFile(alignment);
-      } else {
-        throw new Exception("Implementation error: Unknown file format string");
+      }
+      else
+      {
+        throw new Exception(
+                "Implementation error: Unknown file format string");
       }
 
       afile.addJVSuffix(jvsuffix);
 
       afile.setSeqs(alignment.getSequencesArray());
 
-      return afile.print();
-    }
-    catch (Exception e)
+      String afileresp = afile.print();
+      if (afile.hasWarningMessage())
+      {
+        System.err.println("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");
+      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.");
+            try
+            {
+              System.out.println(new AppletFormatAdapter().formatSequences(
+                      "FASTA", al, true));
+            } catch (Exception e)
+            {
+              System.err
+                      .println("Couln't format the alignment for output as a FASTA file.");
+              e.printStackTrace(System.err);
+            }
+          }
+          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++;
+    }
+  }
+
+  /**
+   * 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
+   */
+  public static String resolveProtocol(String file, String format)
+  {
+    return resolveProtocol(file, format, false);
+  }
+
+  public static String resolveProtocol(String file, String format,
+          boolean debug)
+  {
+    // TODO: test thoroughly!
+    String protocol = null;
+    if (debug)
+    {
+      System.out.println("resolving datasource started with:\n>>file\n"
+              + file + ">>endfile");
+    }
+
+    // This might throw a security exception in certain browsers
+    // Netscape Communicator for instance.
+    try
+    {
+      boolean rtn = false;
+      InputStream is = System.getSecurityManager().getClass()
+              .getResourceAsStream("/" + file);
+      if (is != null)
+      {
+        rtn = true;
+        is.close();
+      }
+      if (debug)
+      {
+        System.err.println("Resource '" + file + "' was "
+                + (rtn ? "" : "not") + " located by classloader.");
+      }
+      ;
+      if (rtn)
+      {
+        protocol = AppletFormatAdapter.CLASSLOADER;
+      }
+
+    } catch (Exception ex)
+    {
+      System.err
+              .println("Exception checking resources: " + file + " " + ex);
+    }
+
+    if (file.indexOf("://") > -1)
+    {
+      protocol = AppletFormatAdapter.URL;
+    }
+    else
+    {
+      // skipping codebase prepend check.
+      protocol = AppletFormatAdapter.FILE;
+    }
+    FileParse fp = null;
+    try
+    {
+      if (debug)
+      {
+        System.out.println("Trying to get contents of resource as "
+                + protocol + ":");
+      }
+      fp = new FileParse(file, protocol);
+      if (!fp.isValid())
+      {
+        fp = null;
+      } else {
+      if (debug)
+      {
+        System.out.println("Successful.");
+      }}
+    } catch (Exception e)
+    {
+      if (debug)
+      {
+        System.err.println("Exception when accessing content: " + e);
+      }
+      fp = null;
+    }
+    if (fp == null)
+    {
+      if (debug)
+      {
+        System.out.println("Accessing as paste.");
+      }
+      protocol = AppletFormatAdapter.PASTE;
+      fp = null;
+      try
+      {
+        fp = new FileParse(file, protocol);
+        if (!fp.isValid())
+        {
+          fp = null;
+        }
+      } catch (Exception e)
+      {
+        System.err.println("Failed to access content as paste!");
+        e.printStackTrace();
+        fp = null;
+      }
+    }
+    if (fp == null)
+    {
+      return null;
+    }
+    if (format == null || format.length() == 0)
+    {
+      return protocol;
+    }
+    else
+    {
+      try
+      {
+        String idformat = new jalview.io.IdentifyFile().Identify(file,
+                protocol);
+        if (idformat == null)
+        {
+          if (debug)
+          {
+            System.out.println("Format not identified. Inaccessible file.");
+          }
+          return null;
+        }
+        if (debug)
+        {
+          System.out.println("Format identified as " + idformat
+                  + "and expected as " + format);
+        }
+        if (idformat.equals(format))
+        {
+          if (debug)
+          {
+            System.out.println("Protocol identified as " + protocol);
+          }
+          return protocol;
+        }
+        else
+        {
+          if (debug)
+          {
+            System.out
+                    .println("File deemed not accessible via " + protocol);
+          }
+          fp.close();
+          return null;
+        }
+      } catch (Exception e)
+      {
+        if (debug)
+        {
+          System.err.println("File deemed not accessible via " + protocol);
+          e.printStackTrace();
+        }
+        ;
+
+      }
+    }
+    return null;
+  }
 }