/*
- * 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * 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.*;
* 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);
}
* hash of feature types and colours
* @return features file contents
*/
- public String printJalviewFormat(SequenceI[] seqs, Hashtable visible)
+ public String printJalviewFormat(SequenceI[] seqs, Map<String,Object> visible)
{
return printJalviewFormat(seqs, visible, true, true);
}
* 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();
// 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)
{
* @param visible
* @return
*/
- public String printGFFFormat(SequenceI[] seqs, Hashtable visible)
+ public String printGFFFormat(SequenceI[] seqs, Map<String,Object> visible)
{
return printGFFFormat(seqs, visible, true, true);
}
- public String printGFFFormat(SequenceI[] seqs, Hashtable visible,
+ public String printGFFFormat(SequenceI[] seqs, Map<String,Object> visible,
boolean visOnly, boolean nonpos)
{
StringBuffer out = new StringBuffer();