X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileParse.java;h=68b5d288ee18a512320f12b1f41a918bf035cbe2;hb=df81a9e1abd4d4424d6d24b37d93f17bffd3649c;hp=ed9fb7e5c24fc8b64dcaf39da9058bccefdb6d60;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java index ed9fb7e..68b5d28 100755 --- a/src/jalview/io/FileParse.java +++ b/src/jalview/io/FileParse.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,16 +20,41 @@ */ 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; + +import jalview.ws.dbsources.Pfam; +import jalview.ws.dbsources.Rfam; + /** * implements a random access wrapper around a particular datasource, for * passing to identifyFile and AlignFile objects. */ public class FileParse { + protected static final String SPACE = " "; + + protected static final String TAB = "\t"; + + private static final String GZ_EXT = ".gz"; + /** * text specifying source of data. usually filename or url. */ @@ -37,10 +62,27 @@ public class FileParse 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 = '#'; /** @@ -64,11 +106,11 @@ public class FileParse */ 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; @@ -94,18 +136,20 @@ 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) { @@ -145,7 +189,7 @@ public class FileParse } if (!error) { - if (fileStr.toLowerCase().endsWith(".gz")) + if (fileStr.toLowerCase().endsWith(GZ_EXT)) { try { @@ -156,49 +200,60 @@ public class FileParse { warningMessage = "Failed to resolve as a GZ stream (" + x.getMessage() + ")"; - x.printStackTrace(); + // x.printStackTrace(); } ; } - + dataIn = new BufferedReader(new FileReader(fileStr)); dataName = fileStr; } return error; } - private BufferedReader tryAsGzipSource(InputStream inputStream) throws Exception + + private BufferedReader tryAsGzipSource(InputStream inputStream) + throws Exception { - BufferedReader inData = new BufferedReader(new InputStreamReader(new GZIPInputStream(inputStream))); + 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 + + private boolean checkURLSource(String fileStr) + throws IOException, MalformedURLException { errormessage = "URL NOT FOUND"; URL url = new URL(fileStr); // - // 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; + // GZIPInputStream code borrowed from Aquaria (soon to be open sourced) via + // Kenny Sabir + Exception e = null; + if (isGzipped(fileStr)) + { + try + { + InputStream inputStream = url.openStream(); + dataIn = tryAsGzipSource(inputStream); + dataName = fileStr; + return false; + } catch (Exception ex) + { + e = ex; } } - try { + try + { dataIn = new BufferedReader(new InputStreamReader(url.openStream())); - } catch (IOException q) { - if (e!=null) + } catch (IOException q) + { + if (e != null) { - throw new IOException("Failed to resolve GZIP stream", e); + throw new IOException(MessageManager + .getString("exception.failed_to_resolve_gzip_stream"), e); } throw q; } @@ -208,6 +263,27 @@ public class FileParse } /** + * Answers true if the filename (or URL) has a format which Jalview recognises + * as denoting gzipped content. + *

+ * Currently this means having a ".gz" extension, or ending in "/gzipped" or + * "?gz=1" (used to retrieve gzipped from Pfam and Rfam respectively). + * + * @param filename + * @return + */ + protected static boolean isGzipped(String filename) + { + if (filename == null) + { + return false; + } + String lower = filename.toLowerCase(); + return lower.endsWith(GZ_EXT) || lower.endsWith(Pfam.GZIPPED) + || lower.endsWith(Rfam.GZIPPED); + } + + /** * sets the suffix string (if any) and returns remainder (if suffix was * detected) * @@ -228,23 +304,47 @@ 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 + * @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)) { @@ -253,18 +353,21 @@ 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 { @@ -272,7 +375,9 @@ public class FileParse { checkURLSource(fileStr); if (suffixSeparator == '#') + { extractSuffix(fileStr); // URL lref is stored for later reference. + } } catch (IOException e) { String suffixLess = extractSuffix(fileStr); @@ -299,13 +404,13 @@ 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() @@ -314,7 +419,9 @@ public class FileParse { String suffixLess = extractSuffix(fileStr); if (suffixLess != null) + { is = getClass().getResourceAsStream("/" + suffixLess); + } } if (is != null) { @@ -329,14 +436,15 @@ 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); @@ -356,17 +464,35 @@ 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; @@ -385,19 +511,27 @@ 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")); } } @@ -464,4 +598,64 @@ public class FileParse } 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; + } }