sp_cleanup.add_missing_deprecated_annotations=true
sp_cleanup.add_missing_methods=false
sp_cleanup.add_missing_nls_tags=false
-sp_cleanup.add_missing_override_annotations=false
+sp_cleanup.add_missing_override_annotations=true
sp_cleanup.add_missing_override_annotations_interface_methods=true
sp_cleanup.add_serial_version_id=false
sp_cleanup.always_use_blocks=true
<strong>What's new ?</strong>
</p>
<p>
- Jalview 2.9 has been in development since December 2014. In addition
+ Jalview 2.9.0b1 is a bug fix release for Jalview 2.9, which has been in development since December 2014. In addition
to a multitude of bug fixes and minor improvements (both small, and
rather big!), it also brings major new capabilities for codon-level
analysis of protein alignments and the retrieval and manipulation of
- structural data.</p><p>For the full list of changes, see the
- <a href="releases.html#Jalview.2.9">Jalview 2.9 Release Notes</a>.
+ structural data.</p><p>For the patches since version 2.9 was release, see the
+ <a href="releases.html#Jalview.2.9.0b1">Jalview 2.9.0b1 Release Notes</a>.
</p>
<p>
<strong>Highlights in Jalview 2.9</strong>
.get("label").toString(), alAnnot.get("description")
.toString(), annotations);
alignAnnot.graph = (alAnnot.get("graphType") == null) ? 0 : Integer
- .valueOf(alAnnot.get("graphType")
- .toString());
+ .valueOf(alAnnot.get("graphType").toString());
JSONObject diplaySettings = (JSONObject) alAnnot
.get("annotationSettings");
+/*******************************************************************************
+ * 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.
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ ******************************************************************************/
package jalview.json.binding.biojson.v1;
import com.github.reinert.jjschema.Attributes;
//- Imported classes and packages -/
//---------------------------------/
-
/**
* Class AnnotationColoursDescriptor.
*
//- Imported classes and packages -/
//---------------------------------/
-
/**
* Class FeaturesDescriptor.
*
//- Imported classes and packages -/
//---------------------------------/
-
/**
* Class UserColourSchemeDescriptor.
*
//- Imported classes and packages -/
//---------------------------------/
-
/**
* Class VamsasModelDescriptor.
*
+/*******************************************************************************
+ * 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.
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ ******************************************************************************/
package jalview.util;
import java.io.IOException;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
import java.util.List;
+/*******************************************************************************
+ * 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.
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ ******************************************************************************/
package jalview.bin;
import static org.testng.AssertJUnit.assertEquals;
import org.testng.annotations.Test;
-
public class JalviewLiteTest
{
assertNull(JalviewLite.separatorListToArray("|", "|"));
assertNull(JalviewLite.separatorListToArray("abc", "abc"));
- String [] array = JalviewLite.separatorListToArray("abc|def|ghi|", "|");
+ String[] array = JalviewLite.separatorListToArray("abc|def|ghi|", "|");
assertEquals(3, array.length);
assertEquals("abc", array[0]);
assertEquals("def", array[1]);
public class FeaturesFileTest
{
- static String TestFiles[][] = {
- { "Test example features import/export",
+ static String TestFiles[][] = { { "Test example features import/export",
"examples/uniref50.fa", "examples/exampleFeatures.txt" } };
@Test(groups = { "Functional" })
// map second dna to second protein seq
map = new MapList(new int[] { 20, 20, 22, 23, 24, 26 }, new int[] { 50,
- 51 },
- 3, 1);
+ 51 }, 3, 1);
acf.addMap(cdna.getSequenceAt(1).getDatasetSequence(), protein
.getSequenceAt(1).getDatasetSequence(), map);
+/*******************************************************************************
+ * 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.
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ ******************************************************************************/
package jalview.util;
import static org.testng.AssertJUnit.assertEquals;
+/*******************************************************************************
+ * 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.
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ ******************************************************************************/
//
//========================================================================
//Copyright (c) 1995-2015 Mort Bay Consulting Pty. Ltd.
server.start();
server.join();
}
-}
\ No newline at end of file
+}
git://source.jalview.org / jalview.git / commitdiff