X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=67d50eea97a7b16035c9272a48c585f2d38b3d05;hb=bda1b6a4412a73727de4613cfe3a6829b0fe0804;hp=5301ab6fef6e47ffa96999e863f508949a4035ba;hpb=75963e12376e3dbfc94e6324461024baea68178f;p=jalview.git diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java index 5301ab6..67d50ee 100755 --- a/src/jalview/io/AppletFormatAdapter.java +++ b/src/jalview/io/AppletFormatAdapter.java @@ -1,13 +1,13 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * 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 * * 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 @@ -18,6 +18,7 @@ package jalview.io; import java.io.File; +import java.io.InputStream; import jalview.datamodel.*; @@ -44,39 +45,46 @@ public class AppletFormatAdapter * method */ public static final String[] WRITEABLE_FORMATS = new String[] - { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "AMSA" }; + { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH", + "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", + "sto,stk" }; /** * 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", + "STH" }; /** * 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" - // }; + { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar", + "sto,stk" }; // , + + // ".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" - // }; + { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview", + "Stockholm" };// , + + // "SimpleBLAST" + // }; public static String INVALID_CHARACTERS = "Contains invalid characters"; @@ -114,6 +122,21 @@ public class AppletFormatAdapter String inFile; /** + * character used to write newlines + */ + protected String newline = System.getProperty("line.separator"); + + public void setNewlineString(String nl) + { + newline = nl; + } + + public String getNewlineString() + { + return newline; + } + + /** * check that this format is valid for reading * * @param format @@ -425,7 +448,7 @@ public class AppletFormatAdapter } else if (format.equalsIgnoreCase("STH")) { - afile = new StockholmFile(); + afile = new StockholmFile(alignment); } else if (format.equalsIgnoreCase("AMSA")) { @@ -436,7 +459,7 @@ public class AppletFormatAdapter throw new Exception( "Implementation error: Unknown file format string"); } - + afile.setNewlineString(newline); afile.addJVSuffix(jvsuffix); afile.setSeqs(alignment.getSequencesArray()); @@ -458,6 +481,18 @@ public class AppletFormatAdapter return null; } + public static String checkProtocol(String file) + { + String protocol = FILE; + String ft = file.toLowerCase().trim(); + if (ft.indexOf("http:") == 0 || ft.indexOf("https:") == 0 + || ft.indexOf("file:") == 0) + { + protocol = URL; + } + return protocol; + } + public static void main(String[] args) { int i = 0; @@ -470,44 +505,47 @@ public class AppletFormatAdapter { 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) + String fName = f.getName(); { - System.out.println("Alignment contains " + al.getHeight() - + " sequences and " + al.getWidth() + " columns."); - try + 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(new AppletFormatAdapter().formatSequences( - "FASTA", al, true)); - } catch (Exception e) + 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.err - .println("Couln't format the alignment for output as a FASTA file."); - e.printStackTrace(System.err); + 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"); } - 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 { @@ -516,6 +554,177 @@ public class AppletFormatAdapter } 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; + } + }