X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=81783fc5cc5841267f9dd038663443aae3146bbe;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=98037e47e2314a525f80399ab080e14ea3536f93;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 98037e4..81783fc 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -1,34 +1,42 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
  * Copyright (C) 2014 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 jalview.api.AlignViewportI;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentView;
+import jalview.util.MessageManager;
+
 import java.io.File;
 import java.io.InputStream;
-
-import jalview.datamodel.*;
+import java.util.List;
 
 /**
  * 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 $Revision$
  */
@@ -38,51 +46,48 @@ 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" }; // , "SimpleBLAST" };
+          { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH",
+    "PDB", "JnetFile", "RNAML", PhylipFile.FILE_DESC }; // , "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", "STH",
-      "AMSA" };
+          { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "AMSA",
+    "STH", PhylipFile.FILE_DESC };
 
   /**
    * 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", "jar",
-      "sto,stk" };
+          { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
+    "jvp", "sto,stk", "jar", PhylipFile.FILE_EXT };
 
   /**
    * 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",
-      "STH" };
+          { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview",
+    "STH", "Jalview", PhylipFile.FILE_DESC };
 
   /**
    * 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", "jar",
-      "sto,stk" }; // ,
-
-  // ".blast"
-  // };
+          { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
+    "jar,jvp", "sto,stk", "xml,rnaml", PhylipFile.FILE_EXT }; // ".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" };// ,
+          { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview",
+    "Stockholm", "RNAML", PhylipFile.FILE_DESC };// ,
 
   // "SimpleBLAST"
   // };
@@ -94,7 +99,7 @@ public class AppletFormatAdapter
           + prettyPrint(READABLE_FORMATS);
 
   /**
-   * 
+   *
    * @param els
    * @return grammatically correct(ish) list consisting of els elements.
    */
@@ -118,6 +123,21 @@ public class AppletFormatAdapter
 
   public static String CLASSLOADER = "ClassLoader";
 
+  /**
+   * add jalview-derived non-secondary structure annotation from PDB structure
+   */
+  boolean annotFromStructure = false;
+
+  /**
+   * add secondary structure from PDB data with built-in algorithms
+   */
+  boolean localSecondaryStruct = false;
+
+  /**
+   * process PDB data with web services
+   */
+  boolean serviceSecondaryStruct = false;
+
   AlignFile afile = null;
 
   String inFile;
@@ -139,7 +159,7 @@ public class AppletFormatAdapter
 
   /**
    * 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
@@ -151,7 +171,7 @@ public class AppletFormatAdapter
 
   /**
    * validate format is valid for IO
-   * 
+   *
    * @param format
    *          a format string to be compared with either READABLE_FORMATS or
    *          WRITEABLE_FORMATS
@@ -165,9 +185,9 @@ 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;
       }
@@ -178,14 +198,14 @@ 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)
@@ -231,7 +251,10 @@ public class AppletFormatAdapter
       }
       else if (format.equals("PDB"))
       {
-        afile = new MCview.PDBfile(inFile, type);
+        afile = 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"))
       {
@@ -241,6 +264,14 @@ public class AppletFormatAdapter
       {
         afile = new SimpleBlastFile(inFile, type);
       }
+      else if (format.equals(PhylipFile.FILE_DESC))
+      {
+        afile = new PhylipFile(inFile, type);
+      }
+      else if (format.equals("RNAML"))
+      {
+        afile = new RnamlFile(inFile, type);
+      }
 
       Alignment al = new Alignment(afile.getSeqsAsArray());
 
@@ -288,15 +319,15 @@ 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
@@ -342,17 +373,25 @@ public class AppletFormatAdapter
       }
       else if (format.equals("PDB"))
       {
-        afile = new MCview.PDBfile(source);
+        afile = new MCview.PDBfile(annotFromStructure,
+                localSecondaryStruct, serviceSecondaryStruct, source);
       }
       else if (format.equals("STH"))
       {
         afile = new StockholmFile(source);
       }
+      else if (format.equals("RNAML"))
+      {
+        afile = new RnamlFile(source);
+      }
       else if (format.equals("SimpleBLAST"))
       {
         afile = new SimpleBlastFile(source);
       }
-
+      else if (format.equals(PhylipFile.FILE_DESC))
+      {
+        afile = new PhylipFile(source);
+      }
       Alignment al = new Alignment(afile.getSeqsAsArray());
 
       afile.addAnnotations(al);
@@ -397,11 +436,40 @@ 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
@@ -409,7 +477,7 @@ 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,
@@ -455,10 +523,18 @@ public class AppletFormatAdapter
       {
         afile = new AMSAFile(alignment);
       }
+      else if (format.equalsIgnoreCase(PhylipFile.FILE_DESC))
+      {
+        afile = new PhylipFile();
+      }
+      else if (format.equalsIgnoreCase("RNAML"))
+      {
+        afile = new RnamlFile();
+      }
+
       else
       {
-        throw new Exception(
-                "Implementation error: Unknown file format string");
+        throw new Exception(MessageManager.getString("error.implementation_error_unknown_file_format_string"));
       }
       afile.setNewlineString(newline);
       afile.addJVSuffix(jvsuffix);
@@ -506,47 +582,43 @@ public class AppletFormatAdapter
         {
           System.out.println("Reading file: " + f);
           AppletFormatAdapter afa = new AppletFormatAdapter();
-          String fName = f.getName();
+          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)
           {
-            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("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(new AppletFormatAdapter().formatSequences(
+                      "FASTA", al, true));
+            } catch (Exception e)
             {
-              System.out.println("Couldn't read alignment");
+              System.err
+              .println("Couln't format the alignment for output as a FASTA file.");
+              e.printStackTrace(System.err);
             }
-            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");
           }
+          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
       {
@@ -560,7 +632,7 @@ 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
@@ -607,7 +679,7 @@ public class AppletFormatAdapter
     } catch (Exception ex)
     {
       System.err
-              .println("Exception checking resources: " + file + " " + ex);
+      .println("Exception checking resources: " + file + " " + ex);
     }
 
     if (file.indexOf("://") > -1)
@@ -709,7 +781,7 @@ 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;
@@ -727,5 +799,4 @@ public class AppletFormatAdapter
     }
     return null;
   }
-
 }