X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFeaturesFile.java;h=804cefc682381bc37a41d3cf15849d3317dbe8b2;hb=25aaaa87042b3f507ad4348120df7dd073182759;hp=afbd22324cf3fb605c67cd54dae9a39e61a7ba3f;hpb=3e7ebcfda0bc54b3b91905e21835142bfd1fe8a0;p=jalview.git
diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index afbd223..804cefc 100755
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -1,34 +1,28 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
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.*;
@@ -68,26 +62,13 @@ public class FeaturesFile extends AlignFile
*
* @throws IOException
* DOCUMENT ME!
- * @throws SAXException
- * @throws ParserConfigurationException
- * @throws ExceptionFileFormatOrSyntax
- * @throws ExceptionLoadingFailed
- * @throws ExceptionPermissionDenied
- * @throws InterruptedException
- * @throws ExceptionUnmatchedClosingParentheses
*/
- public FeaturesFile(String inFile, String type) throws IOException,
- ExceptionFileFormatOrSyntax, ParserConfigurationException,
- SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed,
- InterruptedException, ExceptionUnmatchedClosingParentheses
+ public FeaturesFile(String inFile, String type) throws IOException
{
super(inFile, type);
}
- public FeaturesFile(FileParse source) throws IOException,
- ExceptionFileFormatOrSyntax, ParserConfigurationException,
- SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed,
- InterruptedException, ExceptionUnmatchedClosingParentheses
+ public FeaturesFile(FileParse source) throws IOException
{
super(source);
}
@@ -151,7 +132,7 @@ public class FeaturesFile extends AlignFile
}
/**
- * /** Parse GFF or sequence features file
+ * Parse GFF or sequence features file
*
* @param align
* - alignment/dataset containing sequences that are to be annotated
@@ -628,7 +609,6 @@ public class FeaturesFile extends AlignFile
resetMatcher();
} catch (Exception ex)
{
- System.out.println(line);
System.out.println("Error parsing feature file: " + ex + "\n" + line);
ex.printStackTrace(System.err);
resetMatcher();
@@ -698,7 +678,7 @@ public class FeaturesFile extends AlignFile
* hash of feature types and colours
* @return features file contents
*/
- public String printJalviewFormat(SequenceI[] seqs, Hashtable visible)
+ public String printJalviewFormat(SequenceI[] seqs, Map visible)
{
return printJalviewFormat(seqs, visible, true, true);
}
@@ -717,7 +697,7 @@ public class FeaturesFile extends AlignFile
* of group or type)
* @return features file contents
*/
- public String printJalviewFormat(SequenceI[] seqs, Hashtable visible,
+ public String printJalviewFormat(SequenceI[] seqs, Map visible,
boolean visOnly, boolean nonpos)
{
StringBuffer out = new StringBuffer();
@@ -734,11 +714,11 @@ public class FeaturesFile extends AlignFile
// write feature colours only if we're given them and we are generating
// viewed features
// TODO: decide if feature links should also be written here ?
- Enumeration en = visible.keys();
+ Iterator en = visible.keySet().iterator();
String type, color;
- while (en.hasMoreElements())
+ while (en.hasNext())
{
- type = en.nextElement().toString();
+ type = en.next().toString();
if (visible.get(type) instanceof GraduatedColor)
{
@@ -946,12 +926,12 @@ public class FeaturesFile extends AlignFile
* @param visible
* @return
*/
- public String printGFFFormat(SequenceI[] seqs, Hashtable visible)
+ public String printGFFFormat(SequenceI[] seqs, Map visible)
{
return printGFFFormat(seqs, visible, true, true);
}
- public String printGFFFormat(SequenceI[] seqs, Hashtable visible,
+ public String printGFFFormat(SequenceI[] seqs, Map visible,
boolean visOnly, boolean nonpos)
{
StringBuffer out = new StringBuffer();