/*
* The MIT License
*
* Copyright (c) 2013 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package htsjdk.tribble;
/**
* @author Aaron
*
* The base Tribble exception; this allows external libraries to catch any exception Tribble generates
*
*/
public class TribbleException extends RuntimeException {
// what file or input source we are working from
String source;
public TribbleException(String msg) {
super(msg);
}
public TribbleException(String message, Throwable throwable) {
super(message, throwable);
}
/**
* set the source for the file; where we got lines from
* @param source the source location, usually a file though it could be a http link or other source
*/
public void setSource(String source) {
this.source = source;
}
/**
* override the default message with ours, which attaches the source file in question
* @return a string with our internal error, along with the causitive source file (or other input source)
*/
public String getMessage() {
String ret = super.getMessage();
if ( source != null )
ret = ret + ", for input source: " + source;
return ret;
}
// //////////////////////////////////////////////////////////////////////
// other more specific exceptions generated in Tribble
// //////////////////////////////////////////////////////////////////////
// //////////////////////////////////////////////////////////////////////
// Codec exception
// //////////////////////////////////////////////////////////////////////
// if the line to decode is incorrect
public static class InvalidDecodeLine extends TribbleException {
public InvalidDecodeLine(String message, String line) { super (message + ", line = " + line); }
public InvalidDecodeLine(String message, int lineNo) { super (message + ", at line number " + lineNo); }
}
public static class InvalidHeader extends TribbleException {
public InvalidHeader(String message) { super ("Your input file has a malformed header: " + message); }
}
// capture other internal codec exceptions
public static class InternalCodecException extends TribbleException {
public InternalCodecException(String message) { super (message); }
}
// //////////////////////////////////////////////////////////////////////
// Index exceptions
// //////////////////////////////////////////////////////////////////////
public static class UnableToCreateCorrectIndexType extends TribbleException {
public UnableToCreateCorrectIndexType(String message, Exception e) {
super(message,e);
}
public UnableToCreateCorrectIndexType(String message) {
super(message);
}
}
// //////////////////////////////////////////////////////////////////////
// Source exceptions
// //////////////////////////////////////////////////////////////////////
public static class FeatureFileDoesntExist extends TribbleException {
public FeatureFileDoesntExist(String message, String file) {
super(message);
setSource(file);
}
}
public static class MalformedFeatureFile extends TribbleException {
public MalformedFeatureFile(String message, String f, Exception e) {
super(message,e);
setSource(f);
}
public MalformedFeatureFile(String message, String f) {
super(message);
setSource(f);
}
}
public static class UnableToReadIndexFile extends TribbleException {
public UnableToReadIndexFile(String message, String f, Exception e) {
super(message,e);
setSource(f);
}
}
public static class TabixReaderFailure extends TribbleException {
public TabixReaderFailure(String message, String f, Exception e) {
super(message,e);
setSource(f);
}
public TabixReaderFailure(String message, String f) {
super(message);
setSource(f);
}
}
}