/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 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.
*
import jalview.api.AlignExportSettingI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureSettingsModelI;
import jalview.util.MessageManager;
import java.io.BufferedReader;
*/
protected String suffix = null;
- protected String type = null;
+ protected DataSourceType dataSourceType = null;
protected BufferedReader dataIn = null;
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)
{
}
/**
+ * 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))
{
}
}
}
- else if (type.equals(AppletFormatAdapter.URL))
+ else if (sourceType == DataSourceType.URL)
{
try
{
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()
else
{
errormessage = "PROBABLE IMPLEMENTATION ERROR : Datasource Type given as '"
- + (type != null ? type : "null") + "'";
+ + (sourceType != null ? sourceType : "null") + "'";
error = true;
}
if (dataIn == null || 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();
}
// 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;
+ }
}