X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileParse.java;h=b6f94fd53de717b6c5340c70ae93cb2f3261759e;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=1e6757940b9dda43795a8de37e1292f4ae4077fa;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java index 1e67579..b6f94fd 100755 --- a/src/jalview/io/FileParse.java +++ b/src/jalview/io/FileParse.java @@ -1,25 +1,30 @@ /* - * 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 + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1) + * Copyright (C) 2014 The Jalview Authors * - * 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 file is part of Jalview. * - * 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. + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.io; +import jalview.util.MessageManager; + import java.io.*; import java.net.*; +import java.util.zip.GZIPInputStream; /** * implements a random access wrapper around a particular datasource, for @@ -27,14 +32,35 @@ import java.net.*; */ public class FileParse { + /** + * text specifying source of data. usually filename or url. + */ + private String dataName = "unknown source"; + public File inFile = null; public int index = 1; // sequence counter for FileParse object created from - // same data source + + // same data source protected char suffixSeparator = '#'; /** + * character used to write newlines + */ + protected String newline = System.getProperty("line.separator"); + + public void setNewlineString(String nl) + { + newline = nl; + } + + public String getNewlineString() + { + return newline; + } + + /** * '#' separated string tagged on to end of filename or url that was clipped * off to resolve to valid filename */ @@ -70,8 +96,7 @@ public class FileParse { if (from == null) { - throw new Error( - "Implementation error. Null FileParse in copy constructor"); + throw new Error(MessageManager.getString("error.implementation_error_null_fileparse")); } if (from == this) return; @@ -87,6 +112,7 @@ public class FileParse { mark(); } + dataName = from.dataName; } /** @@ -120,17 +146,75 @@ public class FileParse } if (!error) { + if (fileStr.toLowerCase().endsWith(".gz")) + { + try + { + dataIn = tryAsGzipSource(new FileInputStream(fileStr)); + dataName = fileStr; + return error; + } catch (Exception x) + { + warningMessage = "Failed to resolve as a GZ stream (" + + x.getMessage() + ")"; + x.printStackTrace(); + } + ; + } + dataIn = new BufferedReader(new FileReader(fileStr)); + dataName = fileStr; } return error; } + private BufferedReader tryAsGzipSource(InputStream inputStream) + throws Exception + { + BufferedReader inData = new BufferedReader(new InputStreamReader( + new GZIPInputStream(inputStream))); + inData.mark(2048); + inData.read(); + inData.reset(); + return inData; + } + private boolean checkURLSource(String fileStr) throws IOException, MalformedURLException { errormessage = "URL NOT FOUND"; URL url = new URL(fileStr); - dataIn = new BufferedReader(new InputStreamReader(url.openStream())); + // + // GZIPInputStream code borrowed from Aquaria (soon to be open sourced) via + // Kenny Sabir + Exception e = null; + if (fileStr.toLowerCase().endsWith(".gz")) + { + try + { + InputStream inputStream = url.openStream(); + dataIn = tryAsGzipSource(inputStream); + dataName = fileStr; + return false; + } catch (Exception ex) + { + e = ex; + } + } + + try + { + dataIn = new BufferedReader(new InputStreamReader(url.openStream())); + } catch (IOException q) + { + if (e != null) + { + throw new IOException(MessageManager.getString("exception.failed_to_resolve_gzip_stream"), e); + } + throw q; + } + // record URL as name of datasource. + dataName = fileStr; return false; } @@ -158,10 +242,10 @@ public class FileParse * Create a datasource for input to Jalview. See AppletFormatAdapter for the * types of sources that are handled. * - * @param fileStr - - * datasource locator/content - * @param type - - * protocol of source + * @param fileStr + * - datasource locator/content + * @param type + * - protocol of source * @throws MalformedURLException * @throws IOException */ @@ -180,14 +264,12 @@ public class FileParse { if (checkFileSource(suffixLess)) { - throw new IOException("Problem opening " + inFile - + " (also tried " + suffixLess + ") : " + errormessage); + throw new IOException(MessageManager.formatMessage("exception.problem_opening_file_also_tried", new String[]{inFile.getName(),suffixLess,errormessage})); } } else { - throw new IOException("Problem opening " + inFile + " : " - + errormessage); + throw new IOException(MessageManager.formatMessage("exception.problem_opening_file", new String[]{inFile.getName(),errormessage})); } } } @@ -230,6 +312,7 @@ public class FileParse { errormessage = "PASTE INACCESSIBLE!"; dataIn = new BufferedReader(new StringReader(fileStr)); + dataName = "Paste"; } else if (type.equals(AppletFormatAdapter.CLASSLOADER)) { @@ -245,6 +328,7 @@ public class FileParse if (is != null) { dataIn = new BufferedReader(new java.io.InputStreamReader(is)); + dataName = fileStr; } else { @@ -260,8 +344,7 @@ public class FileParse if (dataIn == null || error) { // pass up the reason why we have no source to read from - throw new IOException("Failed to read data from source:\n" - + errormessage); + throw new IOException(MessageManager.formatMessage("exception.failed_to_read_data_from_source", new String[]{errormessage})); } error = false; dataIn.mark(READAHEAD_LIMIT); @@ -281,7 +364,7 @@ public class FileParse } else { - throw new IOException("Unitialised Source Stream"); + throw new IOException(MessageManager.getString("exception.no_init_source_stream")); } } @@ -289,7 +372,7 @@ public class FileParse { if (!error) return dataIn.readLine(); - throw new IOException("Invalid Source Stream:" + errormessage); + throw new IOException(MessageManager.formatMessage("exception.invalid_source_stream", new String[]{errormessage})); } public boolean isValid() @@ -321,8 +404,7 @@ public class FileParse } else { - throw new IOException( - "Implementation Error: Reset called for invalid source."); + throw new IOException(MessageManager.getString("error.implementation_error_reset_called_for_invalid_source")); } } @@ -356,9 +438,34 @@ public class FileParse } } - public Reader getReader() throws IOException + /** + * @return the dataName + */ + public String getDataName() + { + return dataName; + } + + /** + * set the (human readable) name or URI for this datasource + * + * @param dataname + */ + protected void setDataName(String dataname) + { + dataName = dataname; + } + + /** + * get the underlying bufferedReader for this data source. + * + * @return null if no reader available + * @throws IOException + */ + public Reader getReader() { - if (dataIn != null && dataIn.ready()) + if (dataIn != null) // Probably don't need to test for readiness && + // dataIn.ready()) { return dataIn; }