[med-svn] [Git][med-team/figtree][master] 4 commits: Redefining abstract methods from RootedTree in jebl2

[Pierre Gruet (@pgt)]

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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