X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileParse.java;h=c0328d5f0774d4edebe31a095c333d59adc31667;hb=3d0101179759ef157b088ea135423cd909512d9f;hp=cca8ace2c24f319333e3168f1d5b7da208547d46;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java index cca8ace..c0328d5 100755 --- a/src/jalview/io/FileParse.java +++ b/src/jalview/io/FileParse.java @@ -1,25 +1,43 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ 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 java.io.*; -import java.net.*; +import jalview.api.AlignExportSettingI; +import jalview.api.AlignViewportI; +import jalview.api.AlignmentViewPanel; +import jalview.api.FeatureSettingsModelI; +import jalview.util.MessageManager; + +import java.io.BufferedReader; +import java.io.File; +import java.io.FileInputStream; +import java.io.FileReader; +import java.io.IOException; +import java.io.InputStream; +import java.io.InputStreamReader; +import java.io.Reader; +import java.io.StringReader; +import java.net.MalformedURLException; +import java.net.URL; +import java.util.zip.GZIPInputStream; /** * implements a random access wrapper around a particular datasource, for @@ -27,24 +45,61 @@ 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 + /** + * a viewport associated with the current file operation. May be null. May + * move to different object. + */ + private AlignViewportI viewport; + /** + * specific settings for exporting data from the current context + */ + private AlignExportSettingI exportSettings; + + /** + * sequence counter for FileParse object created from same data source + */ + public int index = 1; + + /** + * separator for extracting specific 'frame' of a datasource for formats that + * support multiple records (e.g. BLC, Stockholm, etc) + */ 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 */ protected String suffix = null; - protected String type = null; + protected DataSourceType dataSourceType = null; protected BufferedReader dataIn = null; - protected String errormessage = "UNITIALISED SOURCE"; + protected String errormessage = "UNINITIALISED SOURCE"; protected boolean error = true; @@ -70,23 +125,26 @@ 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; + } index = ++from.index; inFile = from.inFile; suffixSeparator = from.suffixSeparator; suffix = from.suffix; errormessage = from.errormessage; // inherit potential error messages error = false; // reset any error condition. - type = from.type; + dataSourceType = from.dataSourceType; dataIn = from.dataIn; if (dataIn != null) { mark(); } + dataName = from.dataName; } /** @@ -120,17 +178,76 @@ 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 boolean checkURLSource(String fileStr) throws IOException, - MalformedURLException + 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; } @@ -155,23 +272,47 @@ public class FileParse } /** + * not for general use, creates a fileParse object for an existing reader with + * configurable values for the origin and the type of the source + */ + public FileParse(BufferedReader source, String originString, + DataSourceType sourceType) + { + dataSourceType = sourceType; + error = false; + inFile = null; + dataName = originString; + dataIn = source; + try + { + if (dataIn.markSupported()) + { + dataIn.mark(READAHEAD_LIMIT); + } + } catch (IOException q) + { + + } + } + + /** * 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 sourceType + * - protocol of source * @throws MalformedURLException * @throws IOException */ - public FileParse(String fileStr, String type) + public FileParse(String fileStr, DataSourceType sourceType) throws MalformedURLException, IOException { - this.type = type; + this.dataSourceType = sourceType; error = false; - if (type.equals(AppletFormatAdapter.FILE)) + if (sourceType == DataSourceType.FILE) { if (checkFileSource(fileStr)) { @@ -180,18 +321,21 @@ 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 })); } } } - else if (type.equals(AppletFormatAdapter.URL)) + else if (sourceType == DataSourceType.URL) { try { @@ -199,7 +343,9 @@ public class FileParse { checkURLSource(fileStr); if (suffixSeparator == '#') + { extractSuffix(fileStr); // URL lref is stored for later reference. + } } catch (IOException e) { String suffixLess = extractSuffix(fileStr); @@ -226,12 +372,13 @@ public class FileParse error = true; } } - else if (type.equals(AppletFormatAdapter.PASTE)) + else if (sourceType == DataSourceType.PASTE) { errormessage = "PASTE INACCESSIBLE!"; dataIn = new BufferedReader(new StringReader(fileStr)); + dataName = "Paste"; } - else if (type.equals(AppletFormatAdapter.CLASSLOADER)) + else if (sourceType == DataSourceType.CLASSLOADER) { errormessage = "RESOURCE CANNOT BE LOCATED"; java.io.InputStream is = getClass() @@ -240,11 +387,14 @@ public class FileParse { String suffixLess = extractSuffix(fileStr); if (suffixLess != null) + { is = getClass().getResourceAsStream("/" + suffixLess); + } } if (is != null) { dataIn = new BufferedReader(new java.io.InputStreamReader(is)); + dataName = fileStr; } else { @@ -254,14 +404,15 @@ public class FileParse else { errormessage = "PROBABLE IMPLEMENTATION ERROR : Datasource Type given as '" - + (type != null ? type : "null") + "'"; + + (sourceType != null ? sourceType : "null") + "'"; error = true; } 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); @@ -281,17 +432,35 @@ public class FileParse } else { - throw new IOException("Unitialised Source Stream"); + throw new IOException( + MessageManager.getString("exception.no_init_source_stream")); } } public String nextLine() throws IOException { if (!error) + { return dataIn.readLine(); - throw new IOException("Invalid Source Stream:" + errormessage); + } + throw new IOException(MessageManager + .formatMessage("exception.invalid_source_stream", new String[] + { errormessage })); + } + + /** + * + * @return true if this FileParse is configured for Export only + */ + public boolean isExporting() + { + return !error && dataIn == null; } + /** + * + * @return true if the data source is valid + */ public boolean isValid() { return !error; @@ -310,19 +479,27 @@ public class FileParse } /** - * rewinds the datasource the beginning. + * Rewinds the datasource to the marked point if possible + * + * @param bytesRead * */ - public void reset() throws IOException + public void reset(int bytesRead) throws IOException { + if (bytesRead >= READAHEAD_LIMIT) + { + System.err.println(String.format( + "File reset error: read %d bytes but reset limit is %d", + bytesRead, READAHEAD_LIMIT)); + } if (dataIn != null && !error) { dataIn.reset(); } else { - throw new IOException( - "Implementation Error: Reset called for invalid source."); + throw new IOException(MessageManager.getString( + "error.implementation_error_reset_called_for_invalid_source")); } } @@ -356,12 +533,97 @@ 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; } return null; } + + public AlignViewportI getViewport() + { + return viewport; + } + + public void setViewport(AlignViewportI viewport) + { + this.viewport = viewport; + } + + /** + * @return the currently configured exportSettings for writing data. + */ + public AlignExportSettingI getExportSettings() + { + return exportSettings; + } + + /** + * Set configuration for export of data. + * + * @param exportSettings + * the exportSettings to set + */ + public void setExportSettings(AlignExportSettingI exportSettings) + { + this.exportSettings = exportSettings; + } + + /** + * method overridden by complex file exporter/importers which support + * exporting visualisation and layout settings for a view + * + * @param avpanel + */ + public void configureForView(AlignmentViewPanel avpanel) + { + if (avpanel != null) + { + setViewport(avpanel.getAlignViewport()); + } + // could also set export/import settings + } + + /** + * Returns the preferred feature colour configuration if there is one, else + * null + * + * @return + */ + public FeatureSettingsModelI getFeatureColourScheme() + { + return null; + } + + public DataSourceType getDataSourceType() + { + return dataSourceType; + } }