Temporary fix PhyloGenticTreeParser

src/main/java/io/github/programminglife2016/pl1_2016/parser/BaseTreeNode.java

@@ -2,6 +2,7 @@
 
 import java.util.ArrayList;
 import java.util.List;
+import static java.util.stream.Collectors.*;
 
 /**
  * Class for representing a node in the phylogenetic tree.
@@ -104,6 +105,9 @@ public List<TreeNode> getChildren() {
      */
     @Override
     public String toString() {
-        return String.format("BaseTreeNode{id= %d, weight= %d, children= %d, parent = %d}", id, weight, children, parent);
+        return "[" + this.getId() + " " + this.getWeight()
+                + " {" + children.stream()
+                                 .map(Object::toString)
+                                 .collect(joining(", ")) + "}]";
     }
 }

src/main/java/io/github/programminglife2016/pl1_2016/parser/PhyloGeneticTreeParser.java

@@ -1,6 +1,10 @@
 package io.github.programminglife2016.pl1_2016.parser;
 
+import io.github.programminglife2016.pl1_2016.Launcher;
+
+import java.io.ByteArrayInputStream;
 import java.io.InputStream;
+import java.nio.charset.StandardCharsets;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Scanner;
@@ -15,9 +19,7 @@ public class PhyloGeneticTreeParser implements Parser {
     @Override
     public JsonSerializable parse(InputStream inputStream) {
         String s = inputStreamToString(inputStream);
-        StringTokenizer tokenizer = new StringTokenizer(s, "(:,);", true);
-        TreeNode root = constructTree(null, tokenizer);
-        root = root.getChildren().get(0);
+        TreeNode root = parseTokensFromString(s);
         return null;
     }
 
@@ -28,6 +30,17 @@ private String inputStreamToString(InputStream inputStream) {
         return s;
     }
 
+    /**
+     * Create tree from string.
+     * @param s string representin the tree.
+     * @return root of tree
+     */
+    public TreeNode parseTokensFromString(String s) {
+        StringTokenizer tokenizer = new StringTokenizer(s, "(:,);", true);
+        TreeNode root = constructTree(null, tokenizer);
+        return root.getChildren().get(0);
+    }
+
     /**
      * Construct tree from the input of the String Tokenizer.
      * @param parent parent of the current node.
@@ -57,7 +70,9 @@ public TreeNode constructTree(TreeNode parent, StringTokenizer tokenizer) {
                     current = new BaseTreeNode();
                     break;
                 case ")":
-                    nodes.add(current);
+                    if (!current.getId().equals("-") && current.getWeight() != 0.0) {
+                        nodes.add(current);
+                    }
                     weight = 0;
                     if (tokenizer.hasMoreTokens() && tokenizer.nextToken().equals(":")) {
                         weight = Double.parseDouble(tokenizer.nextToken());
@@ -74,4 +89,18 @@ public TreeNode constructTree(TreeNode parent, StringTokenizer tokenizer) {
         current.setChildren(nodes);
         return current;
     }
+
+    /**
+     * Test parser.
+     * @param args args.
+     */
+    public static void main(String[] args) {
+        System.out.println("PhylgoGenetic Tree Parser");
+        PhyloGeneticTreeParser parser = new PhyloGeneticTreeParser();
+//        String s = "(A: 0.1,B: 0.2,(C:0.3,D:0.4):0.5);";
+        String s = "(A: 0.1,B: 0.2,(C:0.3,(Z:1,Y:2):0.4):0.5);";
+//        parser.parse(Launcher.class.getResourceAsStream("/genomes/340tree.rooted.TKK.nwk"));
+        System.out.println("Done");
+        parser.parse(new ByteArrayInputStream(s.getBytes(StandardCharsets.UTF_8)));
+    }
 }

src/main/resources/genomes/vs

@@ -0,0 +1,206 @@
+let SessionLoad = 1
+if &cp | set nocp | endif
+let s:cpo_save=&cpo
+set cpo&vim
+map! <D-v> *
+map  h
+map <NL> mcOj'c
+map  :CtrlPMRU
+map  <Plug>(ctrlp)
+nnoremap Y y$
+vmap gx <Plug>NetrwBrowseXVis
+nmap gx <Plug>NetrwBrowseX
+map gf :bd!
+map gd :bd
+map gp :bp
+map gn :bn
+nnoremap <F3> :w | exec '!sh run.sh'
+nnoremap <F4> :w | exec '!python '.shellescape('%').''
+vnoremap <silent> <Plug>NetrwBrowseXVis :call netrw#BrowseXVis()
+nnoremap <silent> <Plug>NetrwBrowseX :call netrw#BrowseX(expand((exists("g:netrw_gx")? g:netrw_gx : '<cfile>')),netrw#CheckIfRemote())
+nnoremap <silent> <Plug>(ctrlp) :CtrlP
+vmap <BS> "-d
+vmap <D-x> "*d
+vmap <D-c> "*y
+vmap <D-v> "-d"*P
+nmap <D-v> "*P
+inoremap jj 
+let &cpo=s:cpo_save
+unlet s:cpo_save
+set autochdir
+set autoindent
+set autoread
+set background=dark
+set backspace=eol,start,indent
+set backup
+set expandtab
+set fileencodings=ucs-bom,utf-8,default,latin1
+set helplang=nl
+set hidden
+set ignorecase
+set incsearch
+set laststatus=2
+set mouse=a
+set runtimepath=~/.vim,~/.vim/bundle/Vundle.vim,~/.vim/bundle/vim-airline,~/.vim/bundle/ctrlp.vim,~/.vim/bundle/syntastic,/usr/local/share/vim/vimfiles,/usr/local/share/vim/vim74,/usr/local/share/vim/vimfiles/after,~/.vim/after,~/.vim/bundle/Vundle.vim,~/.vim/bundle/Vundle.vim/after,~/.vim/bundle/vim-airline/after,~/.vim/bundle/ctrlp.vim/after,~/.vim/bundle/syntastic/after
+set scrolloff=4
+set shiftround
+set shiftwidth=4
+set showcmd
+set showmatch
+set showtabline=2
+set smartindent
+set smarttab
+set softtabstop=4
+set statusline=%#warningmsg#%{syntasticstatuslineflag()}%*
+set tabline=%!airline#extensions#tabline#get()
+set tabstop=4
+set whichwrap=b,s,<,>,h,l
+set wildignore=*/tmp/*,*.so,*.swp,*.zip,*.mp3,*.pyc
+let s:so_save = &so | let s:siso_save = &siso | set so=0 siso=0
+let v:this_session=expand("<sfile>:p")
+silent only
+cd ~/ProgrammingLife/PL1-2016/src/main/resources/genomes
+if expand('%') == '' && !&modified && line('$') <= 1 && getline(1) == ''
+  let s:wipebuf = bufnr('%')
+endif
+set shortmess=aoO
+badd +10 ~/ProgrammingLife/PL1-2016/src/main/resources/genomes/metadata.csv
+badd +0 ~/ProgrammingLife/PL1-2016/src/main/resources/genomes/parser.py
+argglobal
+silent! argdel *
+argadd metadata.csv
+edit ~/ProgrammingLife/PL1-2016/src/main/resources/genomes/parser.py
+set splitbelow splitright
+set nosplitbelow
+set nosplitright
+wincmd t
+set winheight=1 winwidth=1
+argglobal
+setlocal keymap=
+setlocal noarabic
+setlocal autoindent
+setlocal backupcopy=
+setlocal nobinary
+setlocal nobreakindent
+setlocal breakindentopt=
+setlocal bufhidden=
+setlocal buflisted
+setlocal buftype=
+setlocal nocindent
+setlocal cinkeys=0{,0},0),:,!^F,o,O,e
+setlocal cinoptions=
+setlocal cinwords=if,else,while,do,for,switch
+setlocal colorcolumn=
+setlocal comments=b:#,fb:-
+setlocal commentstring=#\ %s
+setlocal complete=.,w,b,u,t,i
+setlocal concealcursor=
+setlocal conceallevel=0
+setlocal completefunc=
+setlocal nocopyindent
+setlocal cryptmethod=
+setlocal nocursorbind
+setlocal nocursorcolumn
+setlocal nocursorline
+setlocal define=
+setlocal dictionary=
+setlocal nodiff
+setlocal equalprg=
+setlocal errorformat=
+setlocal expandtab
+if &filetype != 'python'
+setlocal filetype=python
+endif
+setlocal fixendofline
+setlocal foldcolumn=0
+setlocal foldenable
+setlocal foldexpr=0
+setlocal foldignore=#
+setlocal foldlevel=0
+setlocal foldmarker={{{,}}}
+set foldmethod=marker
+setlocal foldmethod=marker
+setlocal foldminlines=1
+setlocal foldnestmax=20
+setlocal foldtext=foldtext()
+setlocal formatexpr=
+setlocal formatoptions=tcq
+setlocal formatlistpat=^\\s*\\d\\+[\\]:.)}\\t\ ]\\s*
+setlocal grepprg=
+setlocal iminsert=0
+setlocal imsearch=0
+setlocal include=^\\s*\\(from\\|import\\)
+setlocal includeexpr=substitute(v:fname,'\\.','/','g')
+setlocal indentexpr=GetPythonIndent(v:lnum)
+setlocal indentkeys=0{,0},:,!^F,o,O,e,<:>,=elif,=except
+setlocal noinfercase
+setlocal iskeyword=@,48-57,_,192-255
+setlocal keywordprg=pydoc
+setlocal nolinebreak
+setlocal nolisp
+setlocal lispwords=
+setlocal nolist
+setlocal makeprg=
+setlocal matchpairs=(:),{:},[:]
+setlocal modeline
+setlocal modifiable
+setlocal nrformats=octal,hex
+set number
+setlocal number
+setlocal numberwidth=4
+setlocal omnifunc=pythoncomplete#Complete
+setlocal path=
+setlocal nopreserveindent
+setlocal nopreviewwindow
+setlocal quoteescape=\\
+setlocal noreadonly
+set relativenumber
+setlocal relativenumber
+setlocal norightleft
+setlocal rightleftcmd=search
+setlocal noscrollbind
+setlocal shiftwidth=4
+setlocal noshortname
+setlocal smartindent
+setlocal softtabstop=4
+setlocal nospell
+setlocal spellcapcheck=[.?!]\\_[\\])'\"\	\ ]\\+
+setlocal spellfile=
+setlocal spelllang=en
+setlocal statusline=%!airline#statusline(1)
+setlocal suffixesadd=.py
+setlocal swapfile
+setlocal synmaxcol=3000
+if &syntax != 'python'
+setlocal syntax=python
+endif
+setlocal tabstop=8
+setlocal tags=
+setlocal textwidth=0
+setlocal thesaurus=
+setlocal noundofile
+setlocal undolevels=-123456
+setlocal nowinfixheight
+setlocal nowinfixwidth
+setlocal wrap
+setlocal wrapmargin=0
+let s:l = 1 - ((0 * winheight(0) + 32) / 65)
+if s:l < 1 | let s:l = 1 | endif
+exe s:l
+normal! zt
+1
+normal! 0
+tabnext 1
+if exists('s:wipebuf')
+  silent exe 'bwipe ' . s:wipebuf
+endif
+unlet! s:wipebuf
+set winheight=1 winwidth=20 shortmess=filnxtToO
+let s:sx = expand("<sfile>:p:r")."x.vim"
+if file_readable(s:sx)
+  exe "source " . fnameescape(s:sx)
+endif
+let &so = s:so_save | let &siso = s:siso_save
+doautoall SessionLoadPost
+unlet SessionLoad
+" vim: set ft=vim :