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JAL-3141 Added Presets options in the Backups Preferences pane, with several presets...
[jalview.git]
/
src
/
jalview
/
io
/
FileParse.java
diff --git
a/src/jalview/io/FileParse.java
b/src/jalview/io/FileParse.java
index
71640f4
..
7117d0f
100755
(executable)
--- a/
src/jalview/io/FileParse.java
+++ b/
src/jalview/io/FileParse.java
@@
-23,6
+23,7
@@
package jalview.io;
import jalview.api.AlignExportSettingI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
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 jalview.util.MessageManager;
import java.io.BufferedReader;
@@
-44,6
+45,10
@@
import java.util.zip.GZIPInputStream;
*/
public class FileParse
{
*/
public class FileParse
{
+ protected static final String SPACE = " ";
+
+ protected static final String TAB = "\t";
+
/**
* text specifying source of data. usually filename or url.
*/
/**
* text specifying source of data. usually filename or url.
*/
@@
-94,7
+99,7
@@
public class FileParse
*/
protected String suffix = null;
*/
protected String suffix = null;
- protected String type = null;
+ protected DataSourceType dataSourceType = null;
protected BufferedReader dataIn = null;
protected BufferedReader dataIn = null;
@@
-124,9
+129,8
@@
public class FileParse
{
if (from == null)
{
{
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 (from == this)
{
@@
-138,7
+142,7
@@
public class FileParse
suffix = from.suffix;
errormessage = from.errormessage; // inherit potential error messages
error = false; // reset any error condition.
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)
{
dataIn = from.dataIn;
if (dataIn != null)
{
@@
-203,16
+207,16
@@
public class FileParse
private BufferedReader tryAsGzipSource(InputStream inputStream)
throws Exception
{
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;
}
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);
{
errormessage = "URL NOT FOUND";
URL url = new URL(fileStr);
@@
-241,10
+245,8
@@
public class FileParse
{
if (e != null)
{
{
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;
}
}
throw q;
}
@@
-278,9
+280,9
@@
public class FileParse
* configurable values for the origin and the type of the source
*/
public FileParse(BufferedReader source, String originString,
* 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;
error = false;
inFile = null;
dataName = originString;
@@
-303,18
+305,18
@@
public class FileParse
*
* @param fileStr
* - datasource locator/content
*
* @param fileStr
* - datasource locator/content
- * @param type
+ * @param sourceType
* - protocol of source
* @throws MalformedURLException
* @throws IOException
*/
* - protocol of source
* @throws MalformedURLException
* @throws IOException
*/
- public FileParse(String fileStr, String type)
+ public FileParse(String fileStr, DataSourceType sourceType)
throws MalformedURLException, IOException
{
throws MalformedURLException, IOException
{
- this.type = type;
+ this.dataSourceType = sourceType;
error = false;
error = false;
- if (type.equals(AppletFormatAdapter.FILE))
+ if (sourceType == DataSourceType.FILE)
{
if (checkFileSource(fileStr))
{
{
if (checkFileSource(fileStr))
{
@@
-325,19
+327,19
@@
public class FileParse
{
throw new IOException(MessageManager.formatMessage(
"exception.problem_opening_file_also_tried",
{
throw new IOException(MessageManager.formatMessage(
"exception.problem_opening_file_also_tried",
- new String[] { inFile.getName(), suffixLess,
- errormessage }));
+ new String[]
+ { inFile.getName(), suffixLess, errormessage }));
}
}
else
{
throw new IOException(MessageManager.formatMessage(
}
}
else
{
throw new IOException(MessageManager.formatMessage(
- "exception.problem_opening_file",
- new String[] { inFile.getName(), errormessage }));
+ "exception.problem_opening_file", new String[]
+ { inFile.getName(), errormessage }));
}
}
}
}
}
}
- else if (type.equals(AppletFormatAdapter.URL))
+ else if (sourceType == DataSourceType.URL)
{
try
{
{
try
{
@@
-374,13
+376,13
@@
public class FileParse
error = true;
}
}
error = true;
}
}
- else if (type.equals(AppletFormatAdapter.PASTE))
+ else if (sourceType == DataSourceType.PASTE)
{
errormessage = "PASTE INACCESSIBLE!";
dataIn = new BufferedReader(new StringReader(fileStr));
dataName = "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()
{
errormessage = "RESOURCE CANNOT BE LOCATED";
java.io.InputStream is = getClass()
@@
-406,15
+408,15
@@
public class FileParse
else
{
errormessage = "PROBABLE IMPLEMENTATION ERROR : Datasource Type given as '"
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(
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 }));
+ "exception.failed_to_read_data_from_source", new String[]
+ { errormessage }));
}
error = false;
dataIn.mark(READAHEAD_LIMIT);
}
error = false;
dataIn.mark(READAHEAD_LIMIT);
@@
-445,9
+447,9
@@
public class FileParse
{
return dataIn.readLine();
}
{
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 }));
}
/**
}
/**
@@
-481,20
+483,27
@@
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
{
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"));
}
}
}
}
@@
-605,4
+614,20
@@
public class FileParse
}
// could also set export/import settings
}
}
// 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;
+ }
}
}