X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileParse.java;h=fddb5659da8e7d737de713f5602f3781cc6ce124;hb=3e29fb36af9c48e07837e32b7e99c081b2461b2f;hp=756ecf0a8a7d4827ba690f838b433b865f32e8e3;hpb=25aaaa87042b3f507ad4348120df7dd073182759;p=jalview.git diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java index 756ecf0..fddb565 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 2.8.2b1) - * 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. * @@ -20,6 +20,10 @@ */ package jalview.io; +import jalview.api.AlignExportSettingI; +import jalview.api.AlignViewportI; +import jalview.api.AlignmentViewPanel; +import jalview.api.FeatureSettingsModelI; import jalview.util.MessageManager; import java.io.BufferedReader; @@ -48,10 +52,26 @@ public class FileParse public File inFile = null; - public int index = 1; // sequence counter for FileParse object created from + /** + * a viewport associated with the current file operation. May be null. May + * move to different object. + */ + private AlignViewportI viewport; - // same data source + /** + * 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 = '#'; /** @@ -61,7 +81,7 @@ public class FileParse public void setNewlineString(String nl) { - newline = nl; + newline = nl; } public String getNewlineString() @@ -79,7 +99,7 @@ public class FileParse protected BufferedReader dataIn = null; - protected String errormessage = "UNITIALISED SOURCE"; + protected String errormessage = "UNINITIALISED SOURCE"; protected boolean error = true; @@ -105,7 +125,9 @@ public class FileParse { if (from == null) { - throw new Error(MessageManager.getString("error.implementation_error_null_fileparse")); + throw new Error( + MessageManager + .getString("error.implementation_error_null_fileparse")); } if (from == this) { @@ -220,7 +242,10 @@ public class FileParse { if (e != null) { - throw new IOException(MessageManager.getString("exception.failed_to_resolve_gzip_stream"), e); + throw new IOException( + MessageManager + .getString("exception.failed_to_resolve_gzip_stream"), + e); } throw q; } @@ -250,6 +275,30 @@ 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, + String typeString) + { + type = typeString; + 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. * @@ -275,12 +324,17 @@ public class FileParse { if (checkFileSource(suffixLess)) { - throw new IOException(MessageManager.formatMessage("exception.problem_opening_file_also_tried", new String[]{inFile.getName(),suffixLess,errormessage})); + throw new IOException(MessageManager.formatMessage( + "exception.problem_opening_file_also_tried", + new String[] { inFile.getName(), suffixLess, + errormessage })); } } else { - throw new IOException(MessageManager.formatMessage("exception.problem_opening_file", new String[]{inFile.getName(),errormessage})); + throw new IOException(MessageManager.formatMessage( + "exception.problem_opening_file", + new String[] { inFile.getName(), errormessage })); } } } @@ -292,7 +346,7 @@ public class FileParse { checkURLSource(fileStr); if (suffixSeparator == '#') - { + { extractSuffix(fileStr); // URL lref is stored for later reference. } } catch (IOException e) @@ -359,7 +413,9 @@ public class FileParse if (dataIn == null || error) { // pass up the reason why we have no source to read from - throw new IOException(MessageManager.formatMessage("exception.failed_to_read_data_from_source", new String[]{errormessage})); + throw new IOException(MessageManager.formatMessage( + "exception.failed_to_read_data_from_source", + new String[] { errormessage })); } error = false; dataIn.mark(READAHEAD_LIMIT); @@ -379,7 +435,8 @@ public class FileParse } else { - throw new IOException(MessageManager.getString("exception.no_init_source_stream")); + throw new IOException( + MessageManager.getString("exception.no_init_source_stream")); } } @@ -389,9 +446,24 @@ public class FileParse { return dataIn.readLine(); } - throw new IOException(MessageManager.formatMessage("exception.invalid_source_stream", new String[]{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; @@ -410,18 +482,28 @@ 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(MessageManager.getString("error.implementation_error_reset_called_for_invalid_source")); + throw new IOException( + MessageManager + .getString("error.implementation_error_reset_called_for_invalid_source")); } } @@ -488,4 +570,59 @@ 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; + } }