-/*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, 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.packed;
+import jalview.api.FeatureColourI;
import jalview.datamodel.AlignmentI;
import jalview.io.AppletFormatAdapter;
import jalview.io.FileParse;
import java.io.BufferedReader;
import java.io.IOException;
import java.util.ArrayList;
-import java.util.Hashtable;
+import java.util.HashMap;
import java.util.List;
public class ParsePackedSet
String fmt = null;
try
{
- fmt = new IdentifyFile().Identify(src, false);
+ fmt = new IdentifyFile().identify(src, false);
} catch (Exception ex)
{
exerror = ex;
{
br = new BufferedReader(src.getReader());
}
- if (new jalview.io.AnnotationFile()
- .parseAnnotationFrom(context.getLastAlignment(), br))
+ // TODO: add columnSelection to context
+ if (new jalview.io.AnnotationFile().parseAnnotationFrom(
+ context.getLastAlignment(), null, br))
{
context.updateSetModified(true);
- } else {
+ }
+ else
+ {
errmsg = "Annotation file contained no data.";
}
// if not, create one.
if (context.featureColours == null)
{
- context.featureColours = new Hashtable();
+ context.featureColours = new HashMap<String, FeatureColourI>();
}
try
{
jalview.io.FeaturesFile ff = new jalview.io.FeaturesFile(src);
- context.updateSetModified(ff.parse(context.getLastAlignment(),
+ context.updateSetModified(ff.parse(context.getLastAlignment(),
context.featureColours, false, context.relaxedIdMatching));
} catch (Exception e)
{
}
}
- if (exerror!=null)
+ if (exerror != null)
{
- if (errmsg!=null && errmsg.length()>0)
+ if (errmsg != null && errmsg.length() > 0)
{
- throw new IOException(errmsg,exerror);
- } else {
- throw new IOException(errmsg,exerror);
+ throw new IOException(errmsg, exerror);
+ }
+ else
+ {
+ throw new IOException(errmsg, exerror);
}
- } else {
- if (errmsg!=null && errmsg.length()>0)
- {
- throw new IOException(errmsg);
}
+ else
+ {
+ if (errmsg != null && errmsg.length() > 0)
+ {
+ throw new IOException(errmsg);
+ }
}
}
if (deuniquify)
// to buffers.
// import with deuniquify info, and compare results to input.
- } else {
+ }
+ else
+ {
if (context.getLastAlignmentSet().isModified())
{
- System.err.println("Initial alignment set was modified and any associated views should be updated.");
+ System.err
+ .println("Initial alignment set was modified and any associated views should be updated.");
}
}
}