[med-svn] [Git][med-team/figtree][master] 4 commits: Redefining abstract methods from RootedTree in jebl2
Pierre Gruet (@pgt)
gitlab at salsa.debian.org
Sun Oct 8 06:36:47 BST 2023
Pierre Gruet pushed to branch master at Debian Med / figtree
Commits:
b38aee0d by Pierre Gruet at 2023-10-07T23:01:01+02:00
Redefining abstract methods from RootedTree in jebl2
- - - - -
c070cdde by Pierre Gruet at 2023-10-07T23:01:14+02:00
Raising Standards version to 4.6.2 (no change)
- - - - -
ff8d4556 by Pierre Gruet at 2023-10-07T23:01:54+02:00
Updating changelog
- - - - -
0d97fb93 by Pierre Gruet at 2023-10-07T23:19:48+02:00
Upload to unstable
- - - - -
4 changed files:
- debian/changelog
- debian/control
- + debian/patches/RootedTree_methods.patch
- debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
@@ -1,8 +1,11 @@
-figtree (1.4.4-6) UNRELEASED; urgency=medium
+figtree (1.4.4-6) unstable; urgency=medium
+ * Team upload
* Refreshing d/copyright
+ * Redefining abstract methods from RootedTree in jebl2
+ * Raising Standards version to 4.6.2 (no change)
- -- Pierre Gruet <pgt at debian.org> Fri, 20 Aug 2021 10:36:41 +0200
+ -- Pierre Gruet <pgt at debian.org> Sat, 07 Oct 2023 23:19:41 +0200
figtree (1.4.4-5) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -14,7 +14,7 @@ Build-Depends: debhelper-compat (= 13),
libjam-java (>= 0.1.20140824),
libtrove-java,
libitext5-java
-Standards-Version: 4.5.0
+Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/figtree
Vcs-Git: https://salsa.debian.org/med-team/figtree.git
Homepage: http://tree.bio.ed.ac.uk/software/figtree/
=====================================
debian/patches/RootedTree_methods.patch
=====================================
@@ -0,0 +1,58 @@
+Description: defining inherited abstract methods from RootedTree.
+ Since jebl2/0.1+git20230701.b3c0f25-1, some methods from RootedTree in jebl2
+ have to be redefined in figtree, which is quite straightforward, as one can
+ look at jebl2 classes themselves to do so.
+Author: Pierre Gruet <pgt at debian.org>
+Forwarded: no
+Last-Update: 2023-10-07
+
+--- a/src/figtree/treeviewer/ReRootedTree.java
++++ b/src/figtree/treeviewer/ReRootedTree.java
+@@ -236,6 +236,40 @@
+ return hasLengths;
+ }
+
++ @Override
++ public int getExternalNodeCount(Node node) {
++ if (isExternal(node)) return 1;
++
++ int externalNodeCount = 0;
++ for (Node child : getChildren(node)) {
++ externalNodeCount += getExternalNodeCount(child);
++ }
++
++ return externalNodeCount;
++ }
++
++ @Override
++ public List<Node> getExternalNodes(Node node) {
++ if (isExternal(node)) return Collections.singletonList(node);
++
++ List<Node> tips = new ArrayList<Node>();
++ for (Node child : getChildren(node)) {
++ tips.addAll(getExternalNodes(child));
++ }
++
++ return tips;
++ }
++
++ @Override
++ public boolean isHeightsKnown() {
++ return heightsKnown;
++ }
++
++ @Override
++ public boolean isLengthsKnown() {
++ return lengthsKnown;
++ }
++
+ /**
+ * @param node the node whose branch length (to its parent) is being requested.
+ * @return the length of the branch to the parent node (0.0 if the node is the root).
+@@ -843,4 +877,4 @@
+ private AttributableHelper helper = null;
+
+ }
+-}
+\ No newline at end of file
++}
=====================================
debian/patches/series
=====================================
@@ -5,3 +5,4 @@ fix_itext_api_change.patch
fix_jebl.patch
0009-add-batik-all.jar.patch
fix_ftbfs.patch
+RootedTree_methods.patch
View it on GitLab: https://salsa.debian.org/med-team/figtree/-/compare/cf589ce608d5a089fc9e359e6eb515bcde673348...0d97fb934efc4b0bcaf538b390df078cefaf531e
--
View it on GitLab: https://salsa.debian.org/med-team/figtree/-/compare/cf589ce608d5a089fc9e359e6eb515bcde673348...0d97fb934efc4b0bcaf538b390df078cefaf531e
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