/*
- * 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.
*
*/
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;
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 = '#';
/**
public void setNewlineString(String nl)
{
- newline = nl;
+ newline = nl;
}
public String getNewlineString()
protected BufferedReader dataIn = null;
- protected String errormessage = "UNITIALISED SOURCE";
+ protected String errormessage = "UNINITIALISED SOURCE";
protected boolean error = true;
{
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)
{
{
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;
}
}
/**
+ * 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.
*
{
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 }));
}
}
}
{
checkURLSource(fileStr);
if (suffixSeparator == '#')
- {
+ {
extractSuffix(fileStr); // URL lref is stored for later reference.
}
} catch (IOException e)
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);
}
else
{
- throw new IOException(MessageManager.getString("exception.no_init_source_stream"));
+ throw new IOException(
+ MessageManager.getString("exception.no_init_source_stream"));
}
}
{
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;
}
/**
- * 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"));
}
}
}
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;
+ }
}
git://source.jalview.org / jalview.git / blobdiff