+/*
+ * 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.appletgui;
-import java.awt.BorderLayout;
-import java.awt.Dimension;
-import java.awt.GridLayout;
-import java.awt.Panel;
-
-import jalview.analysis.AlignmentUtils;
import jalview.api.AlignmentViewPanel;
import jalview.api.ViewStyleI;
import jalview.bin.JalviewLite;
import jalview.structure.StructureSelectionManager;
import jalview.viewmodel.AlignmentViewport;
+import java.awt.BorderLayout;
+import java.awt.Dimension;
+import java.awt.GridLayout;
+import java.awt.Panel;
+
public class SplitFrame extends EmbmenuFrame
{
private static final long serialVersionUID = 1L;
private Panel outermost;
/**
- * Constructor
+ * Constructs the split frame placing cdna in the top half. No 'alignment' is
+ * performed here, this should be done by the calling client if wanted.
*/
public SplitFrame(AlignFrame af1, AlignFrame af2)
{
- topFrame = af1;
- bottomFrame = af2;
+ boolean af1IsNucleotide = af1.viewport.getAlignment().isNucleotide();
+ topFrame = af1IsNucleotide ? af1 : af2;
+ bottomFrame = topFrame == af1 ? af2 : af1;
init();
}
AlignmentViewport protein = !topAlignment.isNucleotide() ? topViewport
: (!bottomAlignment.isNucleotide() ? bottomViewport : null);
- boolean mapped = AlignmentUtils.mapProteinToCdna(
- protein.getAlignment(), cdna.getAlignment());
- if (mapped)
- {
- final StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(topViewport.applet);
- ssm.addMappings(protein.getAlignment().getCodonFrames());
- topViewport.setCodingComplement(bottomViewport);
- ssm.addCommandListener(cdna);
- ssm.addCommandListener(protein);
- }
+ final StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(topViewport.applet);
+ ssm.registerMappings(protein.getAlignment().getCodonFrames());
+ topViewport.setCodingComplement(bottomViewport);
+ ssm.addCommandListener(cdna);
+ ssm.addCommandListener(protein);
/*
- * Now mappings exist, can compute cDNA consensus on protein alignment
+ * Compute cDNA consensus on protein alignment
*/
protein.initComplementConsensus();
AlignmentViewPanel ap = topAlignment.isNucleotide() ? bottomFrame.alignPanel