import jalview.api.AlignExportSettingI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureSettingsModelI;
import jalview.util.MessageManager;
import java.io.BufferedReader;
import java.net.URL;
import java.util.zip.GZIPInputStream;
+
+import jalview.ws.dbsources.Pfam;
+import jalview.ws.dbsources.Rfam;
+
/**
* implements a random access wrapper around a particular datasource, for
* passing to identifyFile and AlignFile objects.
*/
public class FileParse
{
+ protected static final String SPACE = " ";
+
+ protected static final String TAB = "\t";
+
+ private static final String GZ_EXT = ".gz";
+
/**
* text specifying source of data. usually filename or url.
*/
public File inFile = null;
+
/**
* a viewport associated with the current file operation. May be null. May
* move to different object.
public void setNewlineString(String nl)
{
- newline = nl;
+ newline = nl;
}
public String getNewlineString()
*/
protected String suffix = null;
- protected String type = null;
+ protected DataSourceType dataSourceType = null;
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)
{
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)
{
}
if (!error)
{
- if (fileStr.toLowerCase().endsWith(".gz"))
+ if (fileStr.toLowerCase().endsWith(GZ_EXT))
{
try
{
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);
// GZIPInputStream code borrowed from Aquaria (soon to be open sourced) via
// Kenny Sabir
Exception e = null;
- if (fileStr.toLowerCase().endsWith(".gz"))
+ if (isGzipped(fileStr))
{
try
{
{
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;
}
}
/**
+ * Answers true if the filename (or URL) has a format which Jalview recognises
+ * as denoting gzipped content.
+ * <p>
+ * Currently this means having a ".gz" extension, or ending in "/gzipped" or
+ * "?gz=1" (used to retrieve gzipped from Pfam and Rfam respectively).
+ *
+ * @param filename
+ * @return
+ */
+ protected static boolean isGzipped(String filename)
+ {
+ if (filename == null)
+ {
+ return false;
+ }
+ String lower = filename.toLowerCase();
+ return lower.endsWith(GZ_EXT) || lower.endsWith(Pfam.GZIPPED)
+ || lower.endsWith(Rfam.GZIPPED);
+ }
+
+ /**
* sets the suffix string (if any) and returns remainder (if suffix was
* detected)
*
* configurable values for the origin and the type of the source
*/
public FileParse(BufferedReader source, String originString,
- String typeString)
+ DataSourceType sourceType)
{
- type = typeString;
+ dataSourceType = sourceType;
error = false;
inFile = null;
dataName = originString;
*
* @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))
{
{
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.URL)
{
try
{
{
checkURLSource(fileStr);
if (suffixSeparator == '#')
- {
+ {
extractSuffix(fileStr); // URL lref is stored for later reference.
}
} catch (IOException e)
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)
{
// 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 }));
}
/**
}
/**
- * 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"));
}
}
*/
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;
+ }
}
git://source.jalview.org / jalview.git / blobdiff