X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileParse.java;h=13c0f4311854153ddbb07fc1b743b22a0924ae60;hb=006890b02106eb31841e6e84d75f1027434823e0;hp=1ab99dbf75c09595361639ed24cd613e6fc5dfa0;hpb=c6c94d2adb0d156345065b1a7e18e26c7b8dd2b8;p=jalview.git diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java index 1ab99db..13c0f43 100755 --- a/src/jalview/io/FileParse.java +++ b/src/jalview/io/FileParse.java @@ -20,12 +20,15 @@ */ package jalview.io; -import jalview.api.AlignExportSettingI; +import jalview.api.AlignExportSettingsI; import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; +import jalview.api.FeatureSettingsModelI; import jalview.util.MessageManager; +import jalview.util.Platform; import java.io.BufferedReader; +import java.io.ByteArrayInputStream; import java.io.File; import java.io.FileInputStream; import java.io.FileReader; @@ -44,6 +47,10 @@ import java.util.zip.GZIPInputStream; */ public class FileParse { + protected static final String SPACE = " "; + + protected static final String TAB = "\t"; + /** * text specifying source of data. usually filename or url. */ @@ -51,6 +58,12 @@ public class FileParse public File inFile = null; + private byte[] bytes; // from JavaScript + + public byte[] getBytes() + { + return bytes; + } /** * a viewport associated with the current file operation. May be null. May * move to different object. @@ -60,7 +73,7 @@ public class FileParse /** * specific settings for exporting data from the current context */ - private AlignExportSettingI exportSettings; + private AlignExportSettingsI exportSettings; /** * sequence counter for FileParse object created from same data source @@ -80,7 +93,7 @@ public class FileParse public void setNewlineString(String nl) { - newline = nl; + newline = nl; } public String getNewlineString() @@ -94,7 +107,7 @@ public class FileParse */ protected String suffix = null; - protected String type = null; + protected DataSourceType dataSourceType = null; protected BufferedReader dataIn = null; @@ -124,7 +137,8 @@ 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) { @@ -136,7 +150,7 @@ public class FileParse 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) { @@ -201,16 +215,16 @@ public class FileParse 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); @@ -239,7 +253,8 @@ 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; } @@ -269,41 +284,100 @@ 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 file + * - datasource locator/content as File or String + * @param sourceType * - protocol of source * @throws MalformedURLException * @throws IOException */ - public FileParse(String fileStr, String type) + public FileParse(Object file, DataSourceType sourceType) throws MalformedURLException, IOException { - this.type = type; + if (file instanceof File) + { + parse((File) file, ((File) file).getPath(), sourceType, true); + } + else + { + parse(null, file.toString(), sourceType, false); + } + } + + private void parse(File file, String fileStr, DataSourceType sourceType, + boolean isFileObject) throws MalformedURLException, IOException + { + bytes = Platform.getFileBytes(file); + dataSourceType = sourceType; error = false; - if (type.equals(AppletFormatAdapter.FILE)) + if (sourceType == DataSourceType.FILE) { - if (checkFileSource(fileStr)) + + if (bytes != null) + { + // this will be from JavaScript + inFile = file; + dataIn = new BufferedReader(new InputStreamReader(new ByteArrayInputStream(bytes))); + dataName = fileStr; + } + else if (checkFileSource(fileStr)) { String suffixLess = extractSuffix(fileStr); if (suffixLess != null) { 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 })); } } } - else if (type.equals(AppletFormatAdapter.URL)) + else if (sourceType == DataSourceType.RELATIVE_URL) + { + // BH 2018 hack for no support for access-origin + bytes = Platform.getFileAsBytes(fileStr); + dataIn = new BufferedReader(new java.io.InputStreamReader(new ByteArrayInputStream(bytes))); + dataName = fileStr; + + } + else if (sourceType == DataSourceType.URL) { try { @@ -311,7 +385,7 @@ public class FileParse { checkURLSource(fileStr); if (suffixSeparator == '#') - { + { extractSuffix(fileStr); // URL lref is stored for later reference. } } catch (IOException e) @@ -340,13 +414,13 @@ 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() @@ -372,13 +446,16 @@ 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(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); @@ -398,7 +475,8 @@ public class FileParse } else { - throw new IOException(MessageManager.getString("exception.no_init_source_stream")); + throw new IOException( + MessageManager.getString("exception.no_init_source_stream")); } } @@ -408,7 +486,9 @@ 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 })); } /** @@ -442,18 +522,27 @@ 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(MessageManager.getString("error.implementation_error_reset_called_for_invalid_source")); + throw new IOException(MessageManager.getString( + "error.implementation_error_reset_called_for_invalid_source")); } } @@ -534,7 +623,7 @@ public class FileParse /** * @return the currently configured exportSettings for writing data. */ - public AlignExportSettingI getExportSettings() + public AlignExportSettingsI getExportSettings() { return exportSettings; } @@ -545,7 +634,7 @@ public class FileParse * @param exportSettings * the exportSettings to set */ - public void setExportSettings(AlignExportSettingI exportSettings) + public void setExportSettings(AlignExportSettingsI exportSettings) { this.exportSettings = exportSettings; } @@ -558,9 +647,26 @@ public class FileParse */ public void configureForView(AlignmentViewPanel avpanel) { - if (avpanel!=null) { + 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; + } }