X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2Fpacked%2FParsePackedSet.java;h=71999f0639459e665854c9e77cf887e79935ffae;hb=b5f2dfda36c463b93f34db95fe5bc5ff2a1516bf;hp=ac7c6dfc434fd5decf67669711c97f80a99553c5;hpb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;p=jalview.git
diff --git a/src/jalview/io/packed/ParsePackedSet.java b/src/jalview/io/packed/ParsePackedSet.java
index ac7c6df..71999f0 100644
--- a/src/jalview/io/packed/ParsePackedSet.java
+++ b/src/jalview/io/packed/ParsePackedSet.java
@@ -1,22 +1,26 @@
-/*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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 .
- *******************************************************************************/
+ *
+ * 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.packed;
+import jalview.api.FeatureColourI;
import jalview.datamodel.AlignmentI;
import jalview.io.AppletFormatAdapter;
import jalview.io.FileParse;
@@ -27,7 +31,7 @@ import jalview.io.packed.DataProvider.JvDataType;
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
@@ -63,7 +67,7 @@ public class ParsePackedSet
String fmt = null;
try
{
- fmt = new IdentifyFile().Identify(src, false);
+ fmt = new IdentifyFile().identify(src, false);
} catch (Exception ex)
{
exerror = ex;
@@ -120,8 +124,9 @@ public class ParsePackedSet
{
br = new BufferedReader(src.getReader());
}
+ // TODO: add columnSelection to context
if (new jalview.io.AnnotationFile().parseAnnotationFrom(
- context.getLastAlignment(), br))
+ context.getLastAlignment(), null, br))
{
context.updateSetModified(true);
}
@@ -153,7 +158,7 @@ public class ParsePackedSet
// if not, create one.
if (context.featureColours == null)
{
- context.featureColours = new Hashtable();
+ context.featureColours = new HashMap();
}
try
{