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proxy commit for Anne Menard <menard.annec@gmail.com> throw generic exceptions (just...
author
jprocter
<jprocter@compbio.dundee.ac.uk>
Fri, 7 Dec 2012 13:47:06 +0000
(13:47 +0000)
committer
jprocter
<jprocter@compbio.dundee.ac.uk>
Fri, 7 Dec 2012 13:47:06 +0000
(13:47 +0000)
19 files changed:
src/MCview/PDBViewer.java
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src/MCview/PDBfile.java
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src/jalview/appletgui/AlignFrame.java
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src/jalview/gui/AssociatePdbFileWithSeq.java
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src/jalview/gui/PopupMenu.java
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src/jalview/io/AlignFile.java
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src/jalview/io/BLCFile.java
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src/jalview/io/ClustalFile.java
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src/jalview/io/FastaFile.java
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src/jalview/io/FeaturesFile.java
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src/jalview/io/JPredFile.java
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src/jalview/io/MSFfile.java
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src/jalview/io/PIRFile.java
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src/jalview/io/PfamFile.java
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src/jalview/io/PileUpfile.java
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src/jalview/io/SimpleBlastFile.java
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src/jalview/io/StockholmFile.java
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src/jalview/io/TCoffeeScoreFile.java
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test/jalview/io/TCoffeeScoreFileTest.java
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diff --git
a/src/MCview/PDBViewer.java
b/src/MCview/PDBViewer.java
index
b3aae51
..
e79c017
100755
(executable)
--- a/
src/MCview/PDBViewer.java
+++ b/
src/MCview/PDBViewer.java
@@
-21,14
+21,6
@@
import java.io.*;
import java.awt.event.*;
import javax.swing.*;
import java.awt.event.*;
import javax.swing.*;
-import javax.xml.parsers.ParserConfigurationException;
-
-import org.xml.sax.SAXException;
-
-import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
-import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
-import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
-import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
import jalview.datamodel.*;
import jalview.gui.*;
import jalview.datamodel.*;
import jalview.gui.*;
@@
-57,7
+49,7
@@
public class PDBViewer extends JInternalFrame implements Runnable
String tmpPDBFile;
public PDBViewer(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
String tmpPDBFile;
public PDBViewer(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
- AlignmentPanel ap, String protocol) throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+ AlignmentPanel ap, String protocol) throws Exception
{
this.pdbentry = pdbentry;
{
this.pdbentry = pdbentry;
diff --git
a/src/MCview/PDBfile.java
b/src/MCview/PDBfile.java
index
1b3aa8b
..
fb14a46
100755
(executable)
--- a/
src/MCview/PDBfile.java
+++ b/
src/MCview/PDBfile.java
@@
-22,14
+22,6
@@
import java.util.*;
import java.awt.*;
import java.awt.*;
-import javax.xml.parsers.ParserConfigurationException;
-
-import org.xml.sax.SAXException;
-
-import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
-import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
-import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
-import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
import jalview.analysis.AlignSeq;
import jalview.datamodel.*;
import jalview.analysis.AlignSeq;
import jalview.datamodel.*;
@@
-47,12
+39,12
@@
public class PDBfile extends jalview.io.AlignFile
*/
boolean VisibleChainAnnotation = false;
*/
boolean VisibleChainAnnotation = false;
- public PDBfile(String inFile, String inType) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+ public PDBfile(String inFile, String inType) throws Exception
{
super(inFile, inType);
}
{
super(inFile, inType);
}
- public PDBfile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+ public PDBfile(FileParse source) throws Exception
{
super(source);
}
{
super(source);
}
@@
-62,7
+54,7
@@
public class PDBfile extends jalview.io.AlignFile
return null;
}
return null;
}
- public void parse() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+ public void parse() throws Exception
{
// TODO set the filename sensibly - try using data source name.
id = safeName(getDataName());
{
// TODO set the filename sensibly - try using data source name.
id = safeName(getDataName());
diff --git
a/src/jalview/appletgui/AlignFrame.java
b/src/jalview/appletgui/AlignFrame.java
index
6826266
..
e5bd3d6
100644
(file)
--- a/
src/jalview/appletgui/AlignFrame.java
+++ b/
src/jalview/appletgui/AlignFrame.java
@@
-3732,10
+3732,7
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
* @throws InterruptedException
\r
* @throws ExceptionUnmatchedClosingParentheses
\r
*/
\r
* @throws InterruptedException
\r
* @throws ExceptionUnmatchedClosingParentheses
\r
*/
\r
- public boolean loadScoreFile(String source) throws IOException,
\r
- ExceptionFileFormatOrSyntax, ParserConfigurationException,
\r
- SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed,
\r
- InterruptedException, ExceptionUnmatchedClosingParentheses
\r
+ public boolean loadScoreFile(String source) throws Exception
\r
{
\r
\r
TCoffeeScoreFile file = new TCoffeeScoreFile(source,
\r
{
\r
\r
TCoffeeScoreFile file = new TCoffeeScoreFile(source,
\r
diff --git
a/src/jalview/gui/AssociatePdbFileWithSeq.java
b/src/jalview/gui/AssociatePdbFileWithSeq.java
index
22c891d
..
ef7dad0
100644
(file)
--- a/
src/jalview/gui/AssociatePdbFileWithSeq.java
+++ b/
src/jalview/gui/AssociatePdbFileWithSeq.java
@@
-43,15
+43,9
@@
public class AssociatePdbFileWithSeq
* assocate the given PDB file with
* @param choice
* @param sequence
* assocate the given PDB file with
* @param choice
* @param sequence
- * @throws SAXException
- * @throws ParserConfigurationException
- * @throws ExceptionFileFormatOrSyntax
- * @throws ExceptionLoadingFailed
- * @throws ExceptionPermissionDenied
- * @throws InterruptedException
- * @throws ExceptionUnmatchedClosingParentheses
+ * @throws IOException
*/
*/
- public PDBEntry associatePdbWithSeq(String choice, String protocol, SequenceI sequence, boolean prompt) throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+ public PDBEntry associatePdbWithSeq(String choice, String protocol, SequenceI sequence, boolean prompt) throws Exception
{
PDBEntry entry = new PDBEntry();
try
{
PDBEntry entry = new PDBEntry();
try
diff --git
a/src/jalview/gui/PopupMenu.java
b/src/jalview/gui/PopupMenu.java
index
3b43e6b
..
ef19521
100644
(file)
--- a/
src/jalview/gui/PopupMenu.java
+++ b/
src/jalview/gui/PopupMenu.java
@@
-1984,7
+1984,7
@@
public class PopupMenu extends JPopupMenu
oal = null;
}
oal = null;
}
- public void pdbFromFile_actionPerformed() throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+ public void pdbFromFile_actionPerformed() throws IOException
{
jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
{
jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
diff --git
a/src/jalview/io/AlignFile.java
b/src/jalview/io/AlignFile.java
index
cfd37b0
..
c0f8531
100755
(executable)
--- a/
src/jalview/io/AlignFile.java
+++ b/
src/jalview/io/AlignFile.java
@@
-85,15
+85,9
@@
public abstract class AlignFile extends FileParse
* Filename to read from.
* @param type
* What type of file to read from (File, URL)
* Filename to read from.
* @param type
* What type of file to read from (File, URL)
- * @throws SAXException
- * @throws ParserConfigurationException
- * @throws ExceptionFileFormatOrSyntax
- * @throws ExceptionLoadingFailed
- * @throws ExceptionPermissionDenied
- * @throws InterruptedException
- * @throws ExceptionUnmatchedClosingParentheses
+ * @throws Exception
*/
*/
- public AlignFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+ public AlignFile(String inFile, String type) throws Exception
{
super(inFile, type);
initData();
{
super(inFile, type);
initData();
@@
-110,16
+104,9
@@
public abstract class AlignFile extends FileParse
* off.
*
* @param source
* off.
*
* @param source
- * @throws IOException
- * @throws SAXException
- * @throws ParserConfigurationException
- * @throws ExceptionFileFormatOrSyntax
- * @throws ExceptionLoadingFailed
- * @throws ExceptionPermissionDenied
- * @throws InterruptedException
- * @throws ExceptionUnmatchedClosingParentheses
+ * @throws Exception
*/
*/
- public AlignFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+ public AlignFile(FileParse source) throws Exception
{
super(source);
initData();
{
super(source);
initData();
@@
-264,15
+251,9
@@
public abstract class AlignFile extends FileParse
/**
* This method must be implemented to parse the contents of the file.
/**
* This method must be implemented to parse the contents of the file.
- * @throws ExceptionFileFormatOrSyntax
- * @throws SAXException
- * @throws ParserConfigurationException
- * @throws ExceptionLoadingFailed
- * @throws ExceptionPermissionDenied
- * @throws InterruptedException
- * @throws ExceptionUnmatchedClosingParentheses
+
*/
*/
- public abstract void parse() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses;
+ public abstract void parse() throws Exception;
/**
* Print out in alignment file format the Sequences in the seqs Vector.
/**
* Print out in alignment file format the Sequences in the seqs Vector.
diff --git
a/src/jalview/io/BLCFile.java
b/src/jalview/io/BLCFile.java
index
b5617c6
..
71c95b5
100755
(executable)
--- a/
src/jalview/io/BLCFile.java
+++ b/
src/jalview/io/BLCFile.java
@@
-55,23
+55,14
@@
public class BLCFile extends AlignFile
* DOCUMENT ME!
* @param type
* DOCUMENT ME!
* DOCUMENT ME!
* @param type
* DOCUMENT ME!
- *
- * @throws IOException
- * DOCUMENT ME!
- * @throws SAXException
- * @throws ParserConfigurationException
- * @throws ExceptionFileFormatOrSyntax
- * @throws ExceptionLoadingFailed
- * @throws ExceptionPermissionDenied
- * @throws InterruptedException
- * @throws ExceptionUnmatchedClosingParentheses
+ * @throws Exception
*/
*/
- public BLCFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+ public BLCFile(String inFile, String type) throws Exception
{
super(inFile, type);
}
{
super(inFile, type);
}
- public BLCFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+ public BLCFile(FileParse source) throws Exception
{
super(source);
}
{
super(source);
}
diff --git
a/src/jalview/io/ClustalFile.java
b/src/jalview/io/ClustalFile.java
index
d1225c4
..
c789139
100755
(executable)
--- a/
src/jalview/io/ClustalFile.java
+++ b/
src/jalview/io/ClustalFile.java
@@
-39,12
+39,12
@@
public class ClustalFile extends AlignFile
{
}
{
}
- public ClustalFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+ public ClustalFile(String inFile, String type) throws Exception
{
super(inFile, type);
}
{
super(inFile, type);
}
- public ClustalFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+ public ClustalFile(FileParse source) throws Exception
{
super(source);
}
{
super(source);
}
diff --git
a/src/jalview/io/FastaFile.java
b/src/jalview/io/FastaFile.java
index
f413540
..
f809443
100755
(executable)
--- a/
src/jalview/io/FastaFile.java
+++ b/
src/jalview/io/FastaFile.java
@@
-59,23
+59,14
@@
public class FastaFile extends AlignFile
* DOCUMENT ME!
* @param type
* DOCUMENT ME!
* DOCUMENT ME!
* @param type
* DOCUMENT ME!
- *
- * @throws IOException
- * DOCUMENT ME!
- * @throws SAXException
- * @throws ParserConfigurationException
- * @throws ExceptionFileFormatOrSyntax
- * @throws ExceptionLoadingFailed
- * @throws ExceptionPermissionDenied
- * @throws InterruptedException
- * @throws ExceptionUnmatchedClosingParentheses
+ * @throws Exception
*/
*/
- public FastaFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+ public FastaFile(String inFile, String type) throws Exception
{
super(inFile, type);
}
{
super(inFile, type);
}
- public FastaFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+ public FastaFile(FileParse source) throws Exception
{
super(source);
}
{
super(source);
}
diff --git
a/src/jalview/io/FeaturesFile.java
b/src/jalview/io/FeaturesFile.java
index
afbd223
..
c65bded
100755
(executable)
--- a/
src/jalview/io/FeaturesFile.java
+++ b/
src/jalview/io/FeaturesFile.java
@@
-65,29
+65,14
@@
public class FeaturesFile extends AlignFile
* DOCUMENT ME!
* @param type
* DOCUMENT ME!
* DOCUMENT ME!
* @param type
* DOCUMENT ME!
- *
- * @throws IOException
- * DOCUMENT ME!
- * @throws SAXException
- * @throws ParserConfigurationException
- * @throws ExceptionFileFormatOrSyntax
- * @throws ExceptionLoadingFailed
- * @throws ExceptionPermissionDenied
- * @throws InterruptedException
- * @throws ExceptionUnmatchedClosingParentheses
+ * @throws Exception
*/
*/
- public FeaturesFile(String inFile, String type) throws IOException,
- ExceptionFileFormatOrSyntax, ParserConfigurationException,
- SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed,
- InterruptedException, ExceptionUnmatchedClosingParentheses
+ public FeaturesFile(String inFile, String type) throws Exception
{
super(inFile, type);
}
{
super(inFile, type);
}
- public FeaturesFile(FileParse source) throws IOException,
- ExceptionFileFormatOrSyntax, ParserConfigurationException,
- SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed,
- InterruptedException, ExceptionUnmatchedClosingParentheses
+ public FeaturesFile(FileParse source) throws Exception
{
super(source);
}
{
super(source);
}
diff --git
a/src/jalview/io/JPredFile.java
b/src/jalview/io/JPredFile.java
index
509758b
..
fc77ad6
100755
(executable)
--- a/
src/jalview/io/JPredFile.java
+++ b/
src/jalview/io/JPredFile.java
@@
-72,23
+72,14
@@
public class JPredFile extends AlignFile
* DOCUMENT ME!
* @param type
* DOCUMENT ME!
* DOCUMENT ME!
* @param type
* DOCUMENT ME!
- *
- * @throws IOException
- * DOCUMENT ME!
- * @throws SAXException
- * @throws ParserConfigurationException
- * @throws ExceptionFileFormatOrSyntax
- * @throws ExceptionLoadingFailed
- * @throws ExceptionPermissionDenied
- * @throws InterruptedException
- * @throws ExceptionUnmatchedClosingParentheses
+ * @throws Exception
*/
*/
- public JPredFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+ public JPredFile(String inFile, String type) throws Exception
{
super(inFile, type);
}
{
super(inFile, type);
}
- public JPredFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+ public JPredFile(FileParse source) throws Exception
{
super(source);
}
{
super(source);
}
@@
-363,15
+354,9
@@
public class JPredFile extends AlignFile
*
* @param args
* DOCUMENT ME!
*
* @param args
* DOCUMENT ME!
- * @throws SAXException
- * @throws ParserConfigurationException
- * @throws ExceptionFileFormatOrSyntax
- * @throws ExceptionLoadingFailed
- * @throws ExceptionPermissionDenied
- * @throws InterruptedException
- * @throws ExceptionUnmatchedClosingParentheses
+ * @throws Exception
*/
*/
- public static void main(String[] args) throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+ public static void main(String[] args) throws Exception
{
try
{
{
try
{
diff --git
a/src/jalview/io/MSFfile.java
b/src/jalview/io/MSFfile.java
index
c3ee382
..
dcbe37d
100755
(executable)
--- a/
src/jalview/io/MSFfile.java
+++ b/
src/jalview/io/MSFfile.java
@@
-55,23
+55,14
@@
public class MSFfile extends AlignFile
* DOCUMENT ME!
* @param type
* DOCUMENT ME!
* DOCUMENT ME!
* @param type
* DOCUMENT ME!
- *
- * @throws IOException
- * DOCUMENT ME!
- * @throws SAXException
- * @throws ParserConfigurationException
- * @throws ExceptionFileFormatOrSyntax
- * @throws ExceptionLoadingFailed
- * @throws ExceptionPermissionDenied
- * @throws InterruptedException
- * @throws ExceptionUnmatchedClosingParentheses
+ * @throws Exception
*/
*/
- public MSFfile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+ public MSFfile(String inFile, String type) throws Exception
{
super(inFile, type);
}
{
super(inFile, type);
}
- public MSFfile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+ public MSFfile(FileParse source) throws Exception
{
super(source);
}
{
super(source);
}
diff --git
a/src/jalview/io/PIRFile.java
b/src/jalview/io/PIRFile.java
index
cdd0b98
..
d910b0f
100755
(executable)
--- a/
src/jalview/io/PIRFile.java
+++ b/
src/jalview/io/PIRFile.java
@@
-41,12
+41,12
@@
public class PIRFile extends AlignFile
{
}
{
}
- public PIRFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+ public PIRFile(String inFile, String type) throws Exception
{
super(inFile, type);
}
{
super(inFile, type);
}
- public PIRFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+ public PIRFile(FileParse source) throws Exception
{
super(source);
}
{
super(source);
}
diff --git
a/src/jalview/io/PfamFile.java
b/src/jalview/io/PfamFile.java
index
af91390
..
30b5076
100755
(executable)
--- a/
src/jalview/io/PfamFile.java
+++ b/
src/jalview/io/PfamFile.java
@@
-39,12
+39,12
@@
public class PfamFile extends AlignFile
{
}
{
}
- public PfamFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+ public PfamFile(String inFile, String type) throws Exception
{
super(inFile, type);
}
{
super(inFile, type);
}
- public PfamFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+ public PfamFile(FileParse source) throws Exception
{
super(source);
}
{
super(source);
}
diff --git
a/src/jalview/io/PileUpfile.java
b/src/jalview/io/PileUpfile.java
index
3fffab3
..
95fb203
100755
(executable)
--- a/
src/jalview/io/PileUpfile.java
+++ b/
src/jalview/io/PileUpfile.java
@@
-63,23
+63,14
@@
public class PileUpfile extends MSFfile
* DOCUMENT ME!
* @param type
* DOCUMENT ME!
* DOCUMENT ME!
* @param type
* DOCUMENT ME!
- *
- * @throws IOException
- * DOCUMENT ME!
- * @throws SAXException
- * @throws ParserConfigurationException
- * @throws ExceptionFileFormatOrSyntax
- * @throws ExceptionLoadingFailed
- * @throws ExceptionPermissionDenied
- * @throws InterruptedException
- * @throws ExceptionUnmatchedClosingParentheses
+ * @throws Exception
*/
*/
- public PileUpfile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+ public PileUpfile(String inFile, String type) throws Exception
{
super(inFile, type);
}
{
super(inFile, type);
}
- public PileUpfile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+ public PileUpfile(FileParse source) throws Exception
{
super(source);
}
{
super(source);
}
diff --git
a/src/jalview/io/SimpleBlastFile.java
b/src/jalview/io/SimpleBlastFile.java
index
9256283
..
53d2790
100644
(file)
--- a/
src/jalview/io/SimpleBlastFile.java
+++ b/
src/jalview/io/SimpleBlastFile.java
@@
-54,12
+54,12
@@
public class SimpleBlastFile extends AlignFile
{
}
{
}
- public SimpleBlastFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+ public SimpleBlastFile(String inFile, String type) throws Exception
{
super(inFile, type);
}
{
super(inFile, type);
}
- public SimpleBlastFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+ public SimpleBlastFile(FileParse source) throws Exception
{
super(source);
}
{
super(source);
}
diff --git
a/src/jalview/io/StockholmFile.java
b/src/jalview/io/StockholmFile.java
index
07a5c80
..
86cb4ae
100644
(file)
--- a/
src/jalview/io/StockholmFile.java
+++ b/
src/jalview/io/StockholmFile.java
@@
-62,12
+62,12
@@
public class StockholmFile extends AlignFile
{
\r
}
\r
\r
{
\r
}
\r
\r
- public StockholmFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
\r
+ public StockholmFile(String inFile, String type) throws Exception
\r
{
\r
super(inFile, type);
\r
}
\r
\r
{
\r
super(inFile, type);
\r
}
\r
\r
- public StockholmFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
\r
+ public StockholmFile(FileParse source) throws Exception
\r
{
\r
super(source);
\r
}
\r
{
\r
super(source);
\r
}
\r
@@
-85,7
+85,7
@@
public class StockholmFile extends AlignFile
* If there is an error with the input file
\r
* @throws ExceptionUnmatchedClosingParentheses
\r
*/
\r
* If there is an error with the input file
\r
* @throws ExceptionUnmatchedClosingParentheses
\r
*/
\r
- public void parse() throws IOException, ExceptionUnmatchedClosingParentheses
\r
+ public void parse()
\r
{
\r
FileReader fr = null;
\r
fr = new FileReader(inFile);
\r
{
\r
FileReader fr = null;
\r
fr = new FileReader(inFile);
\r
diff --git
a/src/jalview/io/TCoffeeScoreFile.java
b/src/jalview/io/TCoffeeScoreFile.java
index
56994ae
..
9776b56
100644
(file)
--- a/
src/jalview/io/TCoffeeScoreFile.java
+++ b/
src/jalview/io/TCoffeeScoreFile.java
@@
-97,13
+97,13
@@
import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
*/
public class TCoffeeScoreFile extends AlignFile {
*/
public class TCoffeeScoreFile extends AlignFile {
- public TCoffeeScoreFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+ public TCoffeeScoreFile(String inFile, String type) throws Exception
{
super(inFile, type);
}
{
super(inFile, type);
}
- public TCoffeeScoreFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+ public TCoffeeScoreFile(FileParse source) throws Exception
{
super(source);
}
{
super(source);
}
diff --git
a/test/jalview/io/TCoffeeScoreFileTest.java
b/test/jalview/io/TCoffeeScoreFileTest.java
index
ce23728
..
78de7bf
100644
(file)
--- a/
test/jalview/io/TCoffeeScoreFileTest.java
+++ b/
test/jalview/io/TCoffeeScoreFileTest.java
@@
-42,7
+42,7
@@
public class TCoffeeScoreFileTest {
final static File ALIGN_FILE = new File("test/jalview/io/tcoffee.fasta_aln");
@Test
final static File ALIGN_FILE = new File("test/jalview/io/tcoffee.fasta_aln");
@Test
- public void testReadHeader() throws IOException, FileNotFoundException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses {
+ public void testReadHeader() throws Exception {
TCoffeeScoreFile scoreFile = new TCoffeeScoreFile(SCORE_FILE.getPath(),AppletFormatAdapter.FILE);
assertTrue(scoreFile.getWarningMessage(),scoreFile.isValid());
TCoffeeScoreFile scoreFile = new TCoffeeScoreFile(SCORE_FILE.getPath(),AppletFormatAdapter.FILE);
assertTrue(scoreFile.getWarningMessage(),scoreFile.isValid());
@@
-64,7
+64,7
@@
public class TCoffeeScoreFileTest {
@Test
@Test
- public void testWrongFile() throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses {
+ public void testWrongFile() throws Exception {
try {
TCoffeeScoreFile result = new TCoffeeScoreFile(ALIGN_FILE.getPath(), FormatAdapter.FILE);
assertFalse(result.isValid());
try {
TCoffeeScoreFile result = new TCoffeeScoreFile(ALIGN_FILE.getPath(), FormatAdapter.FILE);
assertFalse(result.isValid());
@@
-76,7
+76,7
@@
public class TCoffeeScoreFileTest {
}
@Test
}
@Test
- public void testHeightAndWidth() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses {
+ public void testHeightAndWidth() throws Exception {
TCoffeeScoreFile result = new TCoffeeScoreFile(SCORE_FILE.getPath(), FormatAdapter.FILE);
assertTrue(result.isValid());
assertEquals( 8, result.getHeight() );
TCoffeeScoreFile result = new TCoffeeScoreFile(SCORE_FILE.getPath(), FormatAdapter.FILE);
assertTrue(result.isValid());
assertEquals( 8, result.getHeight() );
@@
-116,7
+116,7
@@
public class TCoffeeScoreFileTest {
}
@Test
}
@Test
- public void testParse() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses {
+ public void testParse() throws Exception {
TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(), FormatAdapter.FILE);
TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(), FormatAdapter.FILE);
@@
-133,7
+133,7
@@
public class TCoffeeScoreFileTest {
@Test
@Test
- public void testGetAsList() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses {
+ public void testGetAsList() throws Exception {
TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),FormatAdapter.FILE);
assertTrue(parser.getWarningMessage(),parser.isValid());
TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),FormatAdapter.FILE);
assertTrue(parser.getWarningMessage(),parser.isValid());
@@
-152,7
+152,7
@@
public class TCoffeeScoreFileTest {
@Test
@Test
- public void testGetAsArray() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses {
+ public void testGetAsArray() throws Exception {
TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),FormatAdapter.FILE);
assertTrue(parser.getWarningMessage(),parser.isValid());
TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),FormatAdapter.FILE);
assertTrue(parser.getWarningMessage(),parser.isValid());