-/*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) 2017 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.ext.archaeopteryx;
-import jalview.analysis.TreeModel;
-import jalview.io.NewickFile;
+import jalview.analysis.TreeBuilder;
+import jalview.datamodel.SequenceI;
+import jalview.gui.Desktop;
+import jalview.viewmodel.AlignmentViewport;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.io.PrintWriter;
+import java.awt.Dimension;
+import java.util.Map;
import org.forester.archaeopteryx.Archaeopteryx;
-
-public class ArchaeopteryxInit
+import org.forester.archaeopteryx.MainFrame;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyNode;
+
+/**
+ * Static class for creating Archaeopteryx tree viewer instances from calculated
+ * trees and letting them be bound to Jalview.
+ *
+ * @author kjvanderheide
+ *
+ */
+public final class ArchaeopteryxInit
{
- private String filePath = "/tmp/jalviewtree.nwk";
-
- private TreeModel tree;
-
- private NewickFile newickTree;
-
- public ArchaeopteryxInit(TreeModel jalviewTreeModel)
- {
- this.tree = jalviewTreeModel;
- this.newickTree = treeToNewick(tree);
- }
-
- public ArchaeopteryxInit(NewickFile newickTreeModel)
+ /**
+ * Test method, should generally not be used as it does not bind the tree to
+ * its alignment
+ *
+ * @param aptxTrees
+ * @return
+ */
+ public static MainFrame createUnboundInstance(final Phylogeny aptxTree)
{
- this.newickTree = newickTreeModel;
+ Phylogeny[] aptxTrees = { aptxTree };
+ return createAptxFrame(aptxTrees);
}
- public void startArchaeopteryx()
+ // public static MainFrame createInstance(final Phylogeny[] aptxTrees,
+ // AlignmentViewport jalviewAlignmentView)
+ // {
+ // return createAptxFrameInJalview(aptxTrees);
+ //
+ // }
+ //
+ // public static MainFrame createInstance(final Phylogeny aptxTree,
+ // final AlignmentViewport jalviewAlignmentView)
+ // {
+ // Phylogeny[] aptxTrees = { aptxTree }; // future possibility to load in
+ // // several trees simultaneously
+ // return createAptxFrameInJalview(aptxTrees);
+ //
+ // }
+
+ public static MainFrame createInstance(
+ final TreeBuilder calculatedTree) // very dense method, to be split up
{
- String newickOutput = newickTree.print(newickTree.hasBootstrap(),
- newickTree.hasDistances(), newickTree.hasRootDistance());
-
- File newickFile = new File(filePath);
- PrintWriter writer;
+ ExternalTreeBuilderI<Phylogeny, PhylogenyNode> aptxTreeBuilder = new ArchaeopteryxTreeBuilder(
+ calculatedTree);
- try
- {
- writer = new PrintWriter(newickFile);
- writer.println(newickOutput);
+ Phylogeny aptxTree = aptxTreeBuilder.buildTree();
+ Phylogeny[] aptxTrees = { aptxTree }; // future possibility to load in
+ // several trees simultaneously
- // System.out.println(writer.checkError());
- writer.close();
+ MainFrame aptxApp = createAptxFrame(aptxTrees);
+
+ bindNodesToJalviewSequences(aptxApp, calculatedTree.getAvport(),
+ aptxTreeBuilder.getAlignmentBoundNodes(),
+ aptxTreeBuilder.getNodesBoundAlignment());
+ return bindFrameToJalview(aptxApp);
- String[] commandLineArgs = { "-open", newickFile.getCanonicalPath() };
- Archaeopteryx.main(commandLineArgs);
-
- } catch (FileNotFoundException e)
- {
- // TODO Auto-generated catch block
- e.printStackTrace();
- } catch (IOException e)
- {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
+ }
- }
- public String getFilePath()
+ public static MainFrame createAptxFrame(
+ final Phylogeny[] aptxTrees)
{
- return filePath;
+ MainFrame aptxApp = Archaeopteryx.createApplication(aptxTrees,
+ "_aptx_jalview_configuration_file", null);
+ return aptxApp;
}
- public void setFilePath(String newFilePath)
+ public static JalviewTreeViewerBindingI<?> bindNodesToJalviewSequences(
+ final MainFrame aptxApp,
+ final AlignmentViewport jalviewAlignViewport,
+ final Map<SequenceI, PhylogenyNode> alignMappedToNodes,
+ final Map<PhylogenyNode, SequenceI> nodesMappedToAlign)
{
- this.filePath = newFilePath;
+ return new JalviewAptxBinding(aptxApp, jalviewAlignViewport,
+ alignMappedToNodes, nodesMappedToAlign);
}
- public TreeModel getTree()
- {
- return tree;
- }
- public void setTree(TreeModel newTree)
+ public static MainFrame bindFrameToJalview(final MainFrame aptxApp)
{
- this.tree = newTree;
- }
+ int width = 400;
+ int height = 550;
+ aptxApp.setMinimumSize(new Dimension(width, height));
- public NewickFile getNewickTree()
- {
- return newickTree;
- }
+ Desktop.addInternalFrame(aptxApp, "Archaeopteryx Tree View", true,
+ width, height, true, true);
- public void setNewickTree(NewickFile newNewickTree)
- {
- this.newickTree = newNewickTree;
- }
+ return aptxApp;
- public static NewickFile treeToNewick(TreeModel tree)
- {
- NewickFile newickTree = new NewickFile(tree.getTopNode(),
- tree.hasBootstrap(), tree.hasDistances(),
- tree.hasRootDistance());
- /* System.out.println(newickTree.print(tree.hasBootstrap(),
- tree.hasDistances(), tree.hasRootDistance()));
-
- System.out.println(newickTree.print(newickTree.hasBootstrap(),
- newickTree.hasDistances(), newickTree.hasRootDistance()));*/
-
- return newickTree;
}
-}
\ No newline at end of file
+
+}
git://source.jalview.org / jalview.git / blobdiff