From 2bd43f464e725844b02a106c2d2f187c2c3655a6 Mon Sep 17 00:00:00 2001 From: jprocter Date: Tue, 4 Dec 2012 16:11:26 +0000 Subject: [PATCH] fix merge conflicts for finess on JAL-1140 (introduced by 1a8f953dd71a9e319e910261927f269d69b4692c) --- src/MCview/PDBViewer.java | 3 +-- src/MCview/PDBfile.java | 7 +++--- src/jalview/appletgui/AlignFrame.java | 19 +------------- src/jalview/datamodel/Annotation.java | 3 --- src/jalview/ext/jmol/PDBFileWithJmol.java | 19 ++------------ src/jalview/gui/AssociatePdbFileWithSeq.java | 35 ++++++++------------------ src/jalview/gui/PopupMenu.java | 17 ++----------- src/jalview/io/AlignFile.java | 19 +++----------- src/jalview/io/BLCFile.java | 17 ++++--------- src/jalview/io/ClustalFile.java | 13 ++-------- src/jalview/io/FastaFile.java | 16 ++++-------- src/jalview/io/FeaturesFile.java | 17 ++++--------- src/jalview/io/JPredFile.java | 20 +++++---------- src/jalview/io/MSFfile.java | 17 ++++--------- src/jalview/io/PIRFile.java | 13 ++-------- src/jalview/io/PfamFile.java | 12 ++------- src/jalview/io/PileUpfile.java | 18 +++++-------- src/jalview/io/RnamlFile.java | 29 ++++++++++++++++----- src/jalview/io/SimpleBlastFile.java | 13 ++-------- src/jalview/io/StockholmFile.java | 2 +- src/jalview/io/TCoffeeScoreFile.java | 13 ++-------- test/jalview/io/TCoffeeScoreFileTest.java | 13 +++++----- 22 files changed, 95 insertions(+), 240 deletions(-) diff --git a/src/MCview/PDBViewer.java b/src/MCview/PDBViewer.java index e79c017..c8dbe66 100755 --- a/src/MCview/PDBViewer.java +++ b/src/MCview/PDBViewer.java @@ -49,8 +49,7 @@ public class PDBViewer extends JInternalFrame implements Runnable String tmpPDBFile; public PDBViewer(PDBEntry pdbentry, SequenceI[] seq, String[] chains, - AlignmentPanel ap, String protocol) throws Exception - + AlignmentPanel ap, String protocol) { this.pdbentry = pdbentry; this.seq = seq; diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java index fc286a8..95dec13 100755 --- a/src/MCview/PDBfile.java +++ b/src/MCview/PDBfile.java @@ -22,7 +22,6 @@ import java.util.*; import java.awt.*; - import jalview.analysis.AlignSeq; import jalview.datamodel.*; import jalview.io.FileParse; @@ -39,12 +38,12 @@ public class PDBfile extends jalview.io.AlignFile */ boolean VisibleChainAnnotation = false; - public PDBfile(String inFile, String inType) throws Exception + public PDBfile(String inFile, String inType) throws IOException { super(inFile, inType); } - public PDBfile(FileParse source) throws Exception + public PDBfile(FileParse source) throws IOException { super(source); } @@ -54,7 +53,7 @@ public class PDBfile extends jalview.io.AlignFile return null; } - public void parse() throws Exception + public void parse() throws IOException { // 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 085c9dd..299d1db 100644 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -83,7 +83,6 @@ import java.awt.event.KeyListener; import java.awt.event.WindowAdapter; import java.awt.event.WindowEvent; import java.io.IOException; -import java.io.InputStreamReader; import java.net.URL; import java.net.URLEncoder; import java.util.Enumeration; @@ -92,15 +91,6 @@ import java.util.List; import java.util.StringTokenizer; import java.util.Vector; -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; - public class AlignFrame extends EmbmenuFrame implements ActionListener, ItemListener, KeyListener { @@ -3720,15 +3710,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, * File/URL/T-COFFEE score file contents * @throws IOException * @return true if alignment was annotated with data from source - * @throws SAXException - * @throws ParserConfigurationException - * @throws ExceptionFileFormatOrSyntax - * @throws ExceptionLoadingFailed - * @throws ExceptionPermissionDenied - * @throws InterruptedException - * @throws ExceptionUnmatchedClosingParentheses */ - public boolean loadScoreFile(String source) throws Exception + public boolean loadScoreFile(String source) throws IOException { TCoffeeScoreFile file = new TCoffeeScoreFile(source, diff --git a/src/jalview/datamodel/Annotation.java b/src/jalview/datamodel/Annotation.java index fd1021f..042e0f7 100755 --- a/src/jalview/datamodel/Annotation.java +++ b/src/jalview/datamodel/Annotation.java @@ -18,9 +18,6 @@ package jalview.datamodel; import java.awt.*; -import java.util.ArrayList; - -import fr.orsay.lri.varna.models.rna.RNA; /** * DOCUMENT ME! diff --git a/src/jalview/ext/jmol/PDBFileWithJmol.java b/src/jalview/ext/jmol/PDBFileWithJmol.java index 962fe3c..1059021 100644 --- a/src/jalview/ext/jmol/PDBFileWithJmol.java +++ b/src/jalview/ext/jmol/PDBFileWithJmol.java @@ -20,13 +20,9 @@ package jalview.ext.jmol; import java.io.IOException; import java.util.Map; -import javax.xml.parsers.ParserConfigurationException; - import org.jmol.api.JmolStatusListener; import org.jmol.api.JmolViewer; import org.jmol.constant.EnumCallback; -import org.jmol.constant.EnumStructure; -import org.jmol.modelset.Chain; import org.jmol.modelset.Group; import org.jmol.modelset.Model; import org.jmol.modelset.ModelSet; @@ -34,12 +30,7 @@ import org.jmol.modelset.Polymer; import org.jmol.modelsetbio.BioPolymer; import org.jmol.viewer.Viewer; import org.openscience.jmol.app.JmolApp; -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.AlignmentAnnotation; import jalview.datamodel.Annotation; import jalview.datamodel.PDBEntry; @@ -62,10 +53,7 @@ public class PDBFileWithJmol extends AlignFile implements Viewer viewer = null; public PDBFileWithJmol(String inFile, String type) - throws ExceptionUnmatchedClosingParentheses, IOException, - ExceptionFileFormatOrSyntax, ParserConfigurationException, - SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, - InterruptedException + throws IOException { super(inFile, type); } @@ -128,10 +116,7 @@ public class PDBFileWithJmol extends AlignFile implements * @see jalview.io.AlignFile#parse() */ @Override - public void parse() throws IOException, ExceptionFileFormatOrSyntax, - ParserConfigurationException, SAXException, - ExceptionPermissionDenied, ExceptionLoadingFailed, - InterruptedException, ExceptionUnmatchedClosingParentheses + public void parse() throws IOException { Viewer jmd = getJmolData(); jmd.openReader(getDataName(), getDataName(), getReader()); diff --git a/src/jalview/gui/AssociatePdbFileWithSeq.java b/src/jalview/gui/AssociatePdbFileWithSeq.java index ef7dad0..4c31ce4 100644 --- a/src/jalview/gui/AssociatePdbFileWithSeq.java +++ b/src/jalview/gui/AssociatePdbFileWithSeq.java @@ -18,15 +18,6 @@ package jalview.gui; import javax.swing.JOptionPane; -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.PDBEntry; import jalview.datamodel.SequenceI; @@ -39,23 +30,19 @@ import jalview.datamodel.SequenceI; public class AssociatePdbFileWithSeq { -/** - * assocate the given PDB file with - * @param choice - * @param sequence - * @throws IOException - */ - public PDBEntry associatePdbWithSeq(String choice, String protocol, SequenceI sequence, boolean prompt) throws Exception + /** + * assocate the given PDB file with + * + * @param choice + * @param sequence + */ + public PDBEntry associatePdbWithSeq(String choice, String protocol, + SequenceI sequence, boolean prompt) { PDBEntry entry = new PDBEntry(); try { - - System.out.println("This is a annotation PDB"); - - - MCview.PDBfile pdbfile = new MCview.PDBfile(choice, - protocol); + MCview.PDBfile pdbfile = new MCview.PDBfile(choice, protocol); if (pdbfile.id == null) { @@ -81,7 +68,7 @@ public class AssociatePdbFileWithSeq { entry.setId(pdbfile.id); } - + } catch (java.io.IOException ex) { ex.printStackTrace(); @@ -90,7 +77,5 @@ public class AssociatePdbFileWithSeq entry.setFile(choice); sequence.getDatasetSequence().addPDBId(entry); return entry; - } - } diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 6bc8daf..9c5a222 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -23,14 +23,6 @@ import java.awt.*; 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.analysis.*; import jalview.commands.*; @@ -1064,12 +1056,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - try { - pdbFromFile_actionPerformed(); - } catch (Exception e1) { - // TODO Auto-generated catch block - e1.printStackTrace(); - } + pdbFromFile_actionPerformed(); } }); // RNAFold.setText("From RNA Fold with predict2D"); @@ -1985,7 +1972,7 @@ public class PopupMenu extends JPopupMenu oal = null; } - public void pdbFromFile_actionPerformed() throws Exception + public void pdbFromFile_actionPerformed() { 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 c0f8531..81d0ae4 100755 --- a/src/jalview/io/AlignFile.java +++ b/src/jalview/io/AlignFile.java @@ -27,15 +27,6 @@ import java.util.Enumeration; import java.util.Hashtable; import java.util.Vector; -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; - /** * DOCUMENT ME! * @@ -85,9 +76,8 @@ public abstract class AlignFile extends FileParse * Filename to read from. * @param type * What type of file to read from (File, URL) - * @throws Exception */ - public AlignFile(String inFile, String type) throws Exception + public AlignFile(String inFile, String type) throws IOException { super(inFile, type); initData(); @@ -104,9 +94,9 @@ public abstract class AlignFile extends FileParse * off. * * @param source - * @throws Exception + * @throws IOException */ - public AlignFile(FileParse source) throws Exception + public AlignFile(FileParse source) throws IOException { super(source); initData(); @@ -251,9 +241,8 @@ public abstract class AlignFile extends FileParse /** * This method must be implemented to parse the contents of the file. - */ - public abstract void parse() throws Exception; + public abstract void parse() throws IOException; /** * 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 71c95b5..5b02b59 100755 --- a/src/jalview/io/BLCFile.java +++ b/src/jalview/io/BLCFile.java @@ -20,15 +20,6 @@ package jalview.io; import java.io.*; import java.util.*; -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.*; /** @@ -55,14 +46,16 @@ public class BLCFile extends AlignFile * DOCUMENT ME! * @param type * DOCUMENT ME! - * @throws Exception + * + * @throws IOException + * DOCUMENT ME! */ - public BLCFile(String inFile, String type) throws Exception + public BLCFile(String inFile, String type) throws IOException { super(inFile, type); } - public BLCFile(FileParse source) throws Exception + public BLCFile(FileParse source) throws IOException { super(source); } diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java index c789139..4ae5e77 100755 --- a/src/jalview/io/ClustalFile.java +++ b/src/jalview/io/ClustalFile.java @@ -20,15 +20,6 @@ package jalview.io; import java.io.*; import java.util.*; -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.util.*; @@ -39,12 +30,12 @@ public class ClustalFile extends AlignFile { } - public ClustalFile(String inFile, String type) throws Exception + public ClustalFile(String inFile, String type) throws IOException { super(inFile, type); } - public ClustalFile(FileParse source) throws Exception + public ClustalFile(FileParse source) throws IOException { super(source); } diff --git a/src/jalview/io/FastaFile.java b/src/jalview/io/FastaFile.java index f809443..0e964b3 100755 --- a/src/jalview/io/FastaFile.java +++ b/src/jalview/io/FastaFile.java @@ -19,14 +19,6 @@ package jalview.io; import java.io.*; -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.*; @@ -59,14 +51,16 @@ public class FastaFile extends AlignFile * DOCUMENT ME! * @param type * DOCUMENT ME! - * @throws Exception + * + * @throws IOException + * DOCUMENT ME! */ - public FastaFile(String inFile, String type) throws Exception + public FastaFile(String inFile, String type) throws IOException { super(inFile, type); } - public FastaFile(FileParse source) throws Exception + public FastaFile(FileParse source) throws IOException { super(source); } diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java index 7b45600..5faf334 100755 --- a/src/jalview/io/FeaturesFile.java +++ b/src/jalview/io/FeaturesFile.java @@ -20,15 +20,6 @@ package jalview.io; import java.io.*; import java.util.*; -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.SequenceIdMatcher; import jalview.datamodel.*; import jalview.schemes.*; @@ -65,14 +56,16 @@ public class FeaturesFile extends AlignFile * DOCUMENT ME! * @param type * DOCUMENT ME! - * @throws Exception + * + * @throws IOException + * DOCUMENT ME! */ - public FeaturesFile(String inFile, String type) throws Exception + public FeaturesFile(String inFile, String type) throws IOException { super(inFile, type); } - public FeaturesFile(FileParse source) throws Exception + public FeaturesFile(FileParse source) throws IOException { super(source); } diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java index fc77ad6..abdfed0 100755 --- a/src/jalview/io/JPredFile.java +++ b/src/jalview/io/JPredFile.java @@ -25,15 +25,6 @@ package jalview.io; import java.io.*; import java.util.*; -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.*; /** @@ -72,14 +63,16 @@ public class JPredFile extends AlignFile * DOCUMENT ME! * @param type * DOCUMENT ME! - * @throws Exception + * + * @throws IOException + * DOCUMENT ME! */ - public JPredFile(String inFile, String type) throws Exception + public JPredFile(String inFile, String type) throws IOException { super(inFile, type); } - public JPredFile(FileParse source) throws Exception + public JPredFile(FileParse source) throws IOException { super(source); } @@ -354,9 +347,8 @@ public class JPredFile extends AlignFile * * @param args * DOCUMENT ME! - * @throws Exception */ - public static void main(String[] args) throws Exception + public static void main(String[] args) { try { diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java index dcbe37d..7c70a09 100755 --- a/src/jalview/io/MSFfile.java +++ b/src/jalview/io/MSFfile.java @@ -20,15 +20,6 @@ package jalview.io; import java.io.*; import java.util.*; -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.util.*; @@ -55,14 +46,16 @@ public class MSFfile extends AlignFile * DOCUMENT ME! * @param type * DOCUMENT ME! - * @throws Exception + * + * @throws IOException + * DOCUMENT ME! */ - public MSFfile(String inFile, String type) throws Exception + public MSFfile(String inFile, String type) throws IOException { super(inFile, type); } - public MSFfile(FileParse source) throws Exception + public MSFfile(FileParse source) throws IOException { super(source); } diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java index d910b0f..9431cc5 100755 --- a/src/jalview/io/PIRFile.java +++ b/src/jalview/io/PIRFile.java @@ -20,15 +20,6 @@ package jalview.io; import java.io.*; import java.util.*; -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.*; public class PIRFile extends AlignFile @@ -41,12 +32,12 @@ public class PIRFile extends AlignFile { } - public PIRFile(String inFile, String type) throws Exception + public PIRFile(String inFile, String type) throws IOException { super(inFile, type); } - public PIRFile(FileParse source) throws Exception + public PIRFile(FileParse source) throws IOException { super(source); } diff --git a/src/jalview/io/PfamFile.java b/src/jalview/io/PfamFile.java index 30b5076..c5ef4f7 100755 --- a/src/jalview/io/PfamFile.java +++ b/src/jalview/io/PfamFile.java @@ -20,14 +20,6 @@ package jalview.io; import java.io.*; import java.util.*; -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.util.*; @@ -39,12 +31,12 @@ public class PfamFile extends AlignFile { } - public PfamFile(String inFile, String type) throws Exception + public PfamFile(String inFile, String type) throws IOException { super(inFile, type); } - public PfamFile(FileParse source) throws Exception + public PfamFile(FileParse source) throws IOException { super(source); } diff --git a/src/jalview/io/PileUpfile.java b/src/jalview/io/PileUpfile.java index 95fb203..39f367b 100755 --- a/src/jalview/io/PileUpfile.java +++ b/src/jalview/io/PileUpfile.java @@ -34,15 +34,6 @@ package jalview.io; */ import java.io.*; -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.util.*; @@ -63,14 +54,17 @@ public class PileUpfile extends MSFfile * DOCUMENT ME! * @param type * DOCUMENT ME! - * @throws Exception + * + * @throws IOException + * DOCUMENT ME! + */ - public PileUpfile(String inFile, String type) throws Exception + public PileUpfile(String inFile, String type) throws IOException { super(inFile, type); } - public PileUpfile(FileParse source) throws Exception + public PileUpfile(FileParse source) throws IOException { super(source); } diff --git a/src/jalview/io/RnamlFile.java b/src/jalview/io/RnamlFile.java index 0029e60..1d14dae 100644 --- a/src/jalview/io/RnamlFile.java +++ b/src/jalview/io/RnamlFile.java @@ -20,6 +20,7 @@ package jalview.io; import java.io.BufferedReader; import java.io.FileNotFoundException; import java.io.FileReader; +import java.io.IOException; import java.util.ArrayList; import java.util.Vector; import java.util.regex.Matcher; @@ -29,20 +30,19 @@ import jalview.analysis.SecStrConsensus; import jalview.analysis.SecStrConsensus.SimpleBP; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.Annotation; -import jalview.datamodel.SecondaryStructureAnnotation; import jalview.datamodel.Sequence; -import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; 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 fr.orsay.lri.varna.factories.RNAFactory; -import fr.orsay.lri.varna.factories.RNAFactory.RNAFileType; import fr.orsay.lri.varna.models.rna.RNA; -import fr.orsay.lri.varna.utils.RNAMLParser; +/** + * @author jimp + * + */ public class RnamlFile extends AlignFile { public int id; public String namefile; @@ -72,8 +72,25 @@ public class RnamlFile extends AlignFile { return r; } + /* (non-Javadoc) + * @see jalview.io.AlignFile#parse() + */ + public void parse() throws IOException + { + // rather than lose exception semantics whilst parsing RNAML with VARNA we + // wrap the routine and catch all exceptions before passing them up the + // chain as an IOException + try { + _parse(); + } catch (Exception x) + { + error=true; + errormessage="Problem parsing data as RNAML ("+x.getMessage()+")"; + throw new IOException("Couldn't parse the datasource as RNAML",x); + } + } @SuppressWarnings("unchecked") - public void parse() throws FileNotFoundException, + public void _parse() throws FileNotFoundException, ExceptionPermissionDenied, ExceptionLoadingFailed, ExceptionFileFormatOrSyntax { diff --git a/src/jalview/io/SimpleBlastFile.java b/src/jalview/io/SimpleBlastFile.java index 53d2790..5cbf78d 100644 --- a/src/jalview/io/SimpleBlastFile.java +++ b/src/jalview/io/SimpleBlastFile.java @@ -20,15 +20,6 @@ package jalview.io; import java.io.*; import java.util.*; -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.*; /** @@ -54,12 +45,12 @@ public class SimpleBlastFile extends AlignFile { } - public SimpleBlastFile(String inFile, String type) throws Exception + public SimpleBlastFile(String inFile, String type) throws IOException { super(inFile, type); } - public SimpleBlastFile(FileParse source) throws Exception + public SimpleBlastFile(FileParse source) throws IOException { super(source); } diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java index 987cdcd..71cc5c5 100644 --- a/src/jalview/io/StockholmFile.java +++ b/src/jalview/io/StockholmFile.java @@ -91,7 +91,7 @@ public class StockholmFile extends AlignFile * If there is an error with the input file * @throws ExceptionUnmatchedClosingParentheses */ - public void parse() throws Exception + public void parse() throws IOException { StringBuffer treeString = new StringBuffer(); diff --git a/src/jalview/io/TCoffeeScoreFile.java b/src/jalview/io/TCoffeeScoreFile.java index 9776b56..158ba6b 100644 --- a/src/jalview/io/TCoffeeScoreFile.java +++ b/src/jalview/io/TCoffeeScoreFile.java @@ -33,15 +33,6 @@ import java.util.Map; import java.util.regex.Matcher; import java.util.regex.Pattern; -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; - /** * A file parse for T-Coffee score ascii format. This file contains the * alignment consensus for each resude in any sequence. @@ -97,13 +88,13 @@ import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses; */ public class TCoffeeScoreFile extends AlignFile { - public TCoffeeScoreFile(String inFile, String type) throws Exception + public TCoffeeScoreFile(String inFile, String type) throws IOException { super(inFile, type); } - public TCoffeeScoreFile(FileParse source) throws Exception + public TCoffeeScoreFile(FileParse source) throws IOException { super(source); } diff --git a/test/jalview/io/TCoffeeScoreFileTest.java b/test/jalview/io/TCoffeeScoreFileTest.java index 78de7bf..b2fbe14 100644 --- 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 - public void testReadHeader() throws Exception { + public void testReadHeader() throws IOException { TCoffeeScoreFile scoreFile = new TCoffeeScoreFile(SCORE_FILE.getPath(),AppletFormatAdapter.FILE); assertTrue(scoreFile.getWarningMessage(),scoreFile.isValid()); @@ -64,7 +64,7 @@ public class TCoffeeScoreFileTest { @Test - public void testWrongFile() throws Exception { + public void testWrongFile() { try { TCoffeeScoreFile result = new TCoffeeScoreFile(ALIGN_FILE.getPath(), FormatAdapter.FILE); assertFalse(result.isValid()); @@ -76,7 +76,7 @@ public class TCoffeeScoreFileTest { } @Test - public void testHeightAndWidth() throws Exception { + public void testHeightAndWidth() throws IOException { TCoffeeScoreFile result = new TCoffeeScoreFile(SCORE_FILE.getPath(), FormatAdapter.FILE); assertTrue(result.isValid()); assertEquals( 8, result.getHeight() ); @@ -116,7 +116,7 @@ public class TCoffeeScoreFileTest { } @Test - public void testParse() throws Exception { + public void testParse() throws IOException { TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(), FormatAdapter.FILE); @@ -133,8 +133,7 @@ public class TCoffeeScoreFileTest { @Test - public void testGetAsList() throws Exception { - + public void testGetAsList() throws IOException { TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),FormatAdapter.FILE); assertTrue(parser.getWarningMessage(),parser.isValid()); List scores = parser.getScoresList(); @@ -152,7 +151,7 @@ public class TCoffeeScoreFileTest { @Test - public void testGetAsArray() throws Exception { + public void testGetAsArray() throws IOException { TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),FormatAdapter.FILE); assertTrue(parser.getWarningMessage(),parser.isValid()); -- 1.7.10.2