X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=d2dc8f333485eea9311ab2c56747c6b9ddc33b71;hb=16342ec2ab61d371ee70f61ac0294f2716fab638;hp=fbfaab131fba87b73e372fff2d5513f1b4676697;hpb=7cb5308c5ec411a566d131993e63abaaf7f7c7b9;p=jalview.git

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index fbfaab1..d2dc8f3 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -1,97 +1,147 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 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.*;
 
 /**
- * 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" };
 
+  /**
+   * 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" };
+
+  /**
+   * 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 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 +152,21 @@ 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 +201,7 @@ public class AppletFormatAdapter
       else if (format.equals("JnetFile"))
       {
         afile = new JPredFile(inFile, type);
-        ( (JPredFile) afile).removeNonSequences();
+        ((JPredFile) afile).removeNonSequences();
       }
       else if (format.equals("PDB"))
       {
@@ -162,15 +217,14 @@ public class AppletFormatAdapter
       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 +240,114 @@ 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);
+      }
+
+      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))
           {
@@ -205,16 +365,19 @@ 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
-   *
+   * 
+   * @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
     {
@@ -255,8 +418,11 @@ 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);
@@ -264,14 +430,64 @@ public class AppletFormatAdapter
       afile.setSeqs(alignment.getSequencesArray());
 
       return afile.print();
-    }
-    catch (Exception e)
+    } 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.");
+          }
+          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++;
+    }
+
+  }
 }