From 351bcc855657b1f0cdf815aa694ac24b8f530b00 Mon Sep 17 00:00:00 2001 From: kjvdheide Date: Tue, 16 Jan 2018 20:21:13 +0000 Subject: [PATCH] JAL-2798 comments --- src/jalview/gui/Jalview2XML.java | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index abb9fa7..b4ded67 100644 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -1116,6 +1116,8 @@ public class Jalview2XML { tree.writeToXml(new File("word")); copyFileToJar(jout, "word", tree.getTreeName()); + jms.addExtTreeViewer(treeView); + } catch (IOException e) { // TODO Auto-generated catch block @@ -1127,6 +1129,7 @@ public class Jalview2XML } + // SAVE ANNOTATIONS /** * store forward refs from an annotationRow to any groups @@ -3560,12 +3563,26 @@ public class Jalview2XML if (loadTreesAndStructures) { loadTrees(jms, view, af, av, ap); + loadExternalTrees(jprovider, jms, av); loadPDBStructures(jprovider, jseqs, af, ap); loadRnaViewers(jprovider, jseqs, ap); } // and finally return. return af; } + + private void loadExternalTrees(jarInputStreamProvider jprovider, + JalviewModelSequence jms, AlignViewport av) + { + for (TreeFrameI externalTreeViewer: jms.getExtTreeViewer()) { + // String treeFile = copyJarEntry(jprovider, errorMessage, "aptx", null); + TreeViewerUtils.addTreeViewFrameToJalview(externalTreeViewer); + + } + + } + + /** * Instantiate and link any saved RNA (Varna) viewers. The state of the Varna -- 1.7.10.2