X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=417dabad168f86c4927a3d4b02d5d7fa57f320dc;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=0a47a196d811d06c66faaa86b7ce1b3e09c6d23e;hpb=ecef9bc6e3c5c651f2e03fe8fb6597b5dc3dcf05;p=jalview.git diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java index 0a47a19..417daba 100755 --- a/src/jalview/io/AppletFormatAdapter.java +++ b/src/jalview/io/AppletFormatAdapter.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8) - * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) + * Copyright (C) 2014 The Jalview Authors * * This file is part of Jalview. * @@ -14,6 +14,7 @@ * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.io; @@ -38,23 +39,22 @@ public class AppletFormatAdapter */ public static final String[] READABLE_FORMATS = new String[] { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH", - "PDB", "JnetFile" }; // , "SimpleBLAST" }; + "PDB", "JnetFile" , "RNAML"}; // , "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" }; /** * 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" }; /** * List of writable formats by the application. Order must correspond with the @@ -62,18 +62,15 @@ public class AppletFormatAdapter */ public static final String[] WRITABLE_FNAMES = new String[] { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview", - "STH" }; + "STH", "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, 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" }; // ".blast" /** * List of readable formats by application in order corresponding to @@ -81,7 +78,7 @@ public class AppletFormatAdapter */ public static final String[] READABLE_FNAMES = new String[] { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview", - "Stockholm" };// , + "Stockholm","RNAML" };// , // "SimpleBLAST" // }; @@ -230,7 +227,9 @@ public class AppletFormatAdapter } else if (format.equals("PDB")) { - afile = new MCview.PDBfile(inFile, type); + afile = new MCview.PDBfile(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")) { @@ -240,7 +239,11 @@ public class AppletFormatAdapter { afile = new SimpleBlastFile(inFile, type); } - + else if (format.equals("RNAML")) + { + afile = new RnamlFile(inFile, type); + } + Alignment al = new Alignment(afile.getSeqsAsArray()); afile.addAnnotations(al); @@ -295,7 +298,7 @@ public class AppletFormatAdapter * * @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 @@ -347,6 +350,10 @@ public class AppletFormatAdapter { afile = new StockholmFile(source); } + else if (format.equals("RNAML")) + { + afile = new RnamlFile(source); + } else if (format.equals("SimpleBLAST")) { afile = new SimpleBlastFile(source); @@ -454,6 +461,11 @@ public class AppletFormatAdapter { afile = new AMSAFile(alignment); } + else if (format.equalsIgnoreCase("RNAML")) + { + afile = new RnamlFile(); + } + else { throw new Exception( @@ -505,47 +517,43 @@ 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 { @@ -726,5 +734,4 @@ public class AppletFormatAdapter } return null; } - }