/*
- * 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 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.io;
-import java.io.*;
-import java.net.*;
+import jalview.api.AlignExportSettingI;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+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;
/**
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 = '#';
/**
protected BufferedReader dataIn = null;
- protected String errormessage = "UNITIALISED SOURCE";
+ protected String errormessage = "UNINITIALISED SOURCE";
protected boolean error = true;
if (from == null)
{
throw new Error(
- "Implementation error. Null FileParse in copy constructor");
+ MessageManager
+ .getString("error.implementation_error_null_fileparse"));
}
if (from == this)
+ {
return;
+ }
index = ++from.index;
inFile = from.inFile;
suffixSeparator = from.suffixSeparator;
{
warningMessage = "Failed to resolve as a GZ stream ("
+ x.getMessage() + ")";
- x.printStackTrace();
+ // x.printStackTrace();
}
;
}
{
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;
}
{
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 }));
}
}
}
{
checkURLSource(fileStr);
if (suffixSeparator == '#')
+ {
extractSuffix(fileStr); // URL lref is stored for later reference.
+ }
} catch (IOException e)
{
String suffixLess = extractSuffix(fileStr);
{
String suffixLess = extractSuffix(fileStr);
if (suffixLess != null)
+ {
is = getClass().getResourceAsStream("/" + suffixLess);
+ }
}
if (is != null)
{
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);
}
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;
else
{
throw new IOException(
- "Implementation Error: Reset called for invalid source.");
+ MessageManager
+ .getString("error.implementation_error_reset_called_for_invalid_source"));
}
}
}
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
+ }
}
git://source.jalview.org / jalview.git / blobdiff