/*\r
- * originally from \r
+ * This file is part of the Vamsas Client version 0.1. \r
+ * Copyright 2009 by Jim Procter, Iain Milne, Pierre Marguerite, \r
+ * Andrew Waterhouse and Dominik Lindner.\r
* \r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
+ * Earlier versions have also been incorporated into Jalview version 2.4 \r
+ * since 2008, and TOPALi version 2 since 2007.\r
+ * \r
+ * The Vamsas Client is free software: you can redistribute it and/or modify\r
+ * it under the terms of the GNU Lesser General Public License as published by\r
+ * the Free Software Foundation, either version 3 of the License, or\r
+ * (at your option) any later version.\r
+ * \r
+ * The Vamsas Client is distributed in the hope that it will be useful,\r
* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ * GNU Lesser General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU Lesser General Public License\r
+ * along with the Vamsas Client. If not, see <http://www.gnu.org/licenses/>.\r
*/\r
-\r
// NewickFile.java\r
// Tree I/O\r
// http://evolution.genetics.washington.edu/phylip/newick_doc.html\r
// TODO: Extended SequenceNodeI to hold parsed NHX strings\r
package uk.ac.vamsas.objects.utils.trees;\r
\r
-\r
import java.io.*;\r
import java.util.Enumeration;\r
import java.util.Hashtable;\r
private boolean RootHasDistance = false;\r
\r
// File IO Flags\r
- boolean ReplaceUnderscores = false;\r
+ boolean ReplaceUnderscores = true;\r
\r
- boolean printRootInfo = false;\r
+ boolean printRootInfo = true; // in case root has anything to preserve\r
\r
private Pattern[] NodeSafeName = new Pattern[] {\r
Pattern.compile("[\\[,:'()]"), // test for requiring quotes\r
Pattern.compile("'"), // escaping quote characters\r
- Pattern.compile("/w") // unqoted whitespace transformation\r
+ Pattern.compile("\\s") // unqoted whitespace transformation\r
};\r
\r
char QuoteChar = '\'';\r
String newickFile = null;\r
\r
/**\r
- * Creates a new NewickFile object.\r
+ * Creates a new NewickFile object\r
* \r
* @param inStr\r
- * DOCUMENT ME!\r
+ * Newick style tree string\r
* \r
* @throws IOException\r
- * DOCUMENT ME!\r
+ * if string is not a valid newick file\r
*/\r
public NewickFile(String inStr) throws IOException {\r
newickFile = inStr;\r
parse();\r
}\r
+\r
public NewickFile(File inFile) throws IOException {\r
- errormessage = "Problem's reading file "+inFile;\r
- dataIn = new java.io.BufferedReader(new InputStreamReader(new java.io.FileInputStream(inFile)));\r
+ errormessage = "Problem's reading file " + inFile;\r
+ dataIn = new java.io.BufferedReader(new InputStreamReader(\r
+ new java.io.FileInputStream(inFile)));\r
parse();\r
}\r
+\r
/**\r
* Creates a new NewickFile object.\r
* \r
public boolean HasRootDistance() {\r
return RootHasDistance;\r
}\r
+\r
/*\r
* hacked out of jalview code\r
*/\r
boolean error;\r
+\r
String errormessage;\r
- java.io.BufferedReader dataIn=null;\r
+\r
+ java.io.BufferedReader dataIn = null;\r
+\r
public String nextLine() throws IOException {\r
- if (dataIn==null)\r
- {\r
+ if (dataIn == null && newickFile == null)\r
+ throw new IOException(\r
+ "IMPLEMENTATION ERROR: NewickFile has not been initialised for reading a newick string.");\r
+ if (dataIn == null) {\r
dataIn = new BufferedReader(new StringReader(newickFile));\r
- error=false;\r
+ error = false;\r
}\r
- else\r
- throw new IOException("IMPLEMENTATION ERROR: NewickFile has not been initialised for reading a newick string.");\r
if (!error)\r
return dataIn.readLine();\r
throw new IOException("Invalid Source Stream:" + errormessage);\r
}\r
+\r
/**\r
- * call this to convert the newick string into a binary node linked tree\r
+ * call this to convert the newick string into a binary node linked tree Note:\r
+ * this is automatically called by the constructors, so you normally wouldn't\r
+ * need to use this.\r
* \r
* @throws IOException\r
* if the newick string cannot be parsed.\r
*/\r
public void parse() throws IOException {\r
String nf;\r
- if (newickFile==null)\r
- {\r
+ if (newickFile == null) {\r
// fill nf with complete tree file\r
\r
StringBuffer file = new StringBuffer();\r
}\r
\r
nf = file.toString();\r
- } else\r
- {\r
+ } else {\r
nf = newickFile;\r
}\r
- \r
\r
root = new SequenceNode();\r
\r
String nodename = null;\r
\r
float DefDistance = (float) 0.001; // @param Default distance for a node -\r
- // very very small\r
- int DefBootstrap = 0; // @param Default bootstrap for a node\r
+ // very very small\r
+ int DefBootstrap = -1; // @param Default bootstrap for a node\r
\r
float distance = DefDistance;\r
int bootstrap = DefBootstrap;\r
\r
boolean ascending = false; // flag indicating that we are leaving the\r
- // current node\r
+ // current node\r
\r
- Pattern majorsyms = Pattern.compile(\r
- "[(\\['),;]");\r
+ Pattern majorsyms = Pattern.compile("[(\\['),;]");\r
\r
Matcher mjsyms = majorsyms.matcher(nf);\r
+ char schar;\r
+ int nextcp = 0;\r
+ int ncp = cp;\r
while (mjsyms.find(cp) && (Error == null)) {\r
int fcp = mjsyms.start();\r
\r
- switch (nf.charAt(fcp)) {\r
- case '[': // Comment or structured/extended NH format info\r
-\r
-\r
- if (nf.indexOf(']',fcp)>-1) {\r
- // Skip the comment field\r
- cp = nf.indexOf(']',fcp);\r
- } else {\r
- Error = ErrorStringrange(Error, "Unterminated comment", 3, fcp, nf);\r
- }\r
-\r
- ;\r
-\r
- break;\r
-\r
+ switch (schar = nf.charAt(fcp)) {\r
case '(':\r
\r
// ascending should not be set\r
\r
break;\r
\r
- case ';':\r
-\r
- if (d != -1) {\r
+ default:\r
+ // Reached termininating root node label.\r
+ if (schar == ';' && d != -1) {\r
Error = ErrorStringrange(Error,\r
"Wayward semicolon (depth=" + d + ")", 7, fcp, nf);\r
}\r
\r
- // cp advanced at the end of default\r
- default:\r
+ // Skip Comment or structured/extended NH format info\r
+ if (schar == '[') {\r
+ if ((nextcp = nf.indexOf(']', fcp)) > -1) {\r
+ // verified that comment is properly terminated.\r
+ // now skip the comment field\r
+ nextcp++;\r
+ break; // go and search for the next node separator, leaving ncp at\r
+ // beginning of node info\r
+ } else {\r
+ Error = ErrorStringrange(Error, "Unterminated comment", 3, fcp, nf);\r
+ nextcp = 0;\r
+ break;\r
+ }\r
+ }\r
\r
- // Parse simpler field strings\r
- String fstring = nf.substring(cp, fcp);\r
- Matcher uqnodename = Pattern.compile("\\b([^' :;\\](),]+)").matcher(fstring);\r
+ // Parse simpler field strings from substring between ncp and node\r
+ // separator\r
+ String fstring = nf.substring(ncp, fcp);\r
+ // extract any comments from the nodeinfo.\r
+ while (fstring.indexOf(']') > -1) {\r
+ int cstart = fstring.indexOf('[');\r
+ int cend = fstring.indexOf(']');\r
+ String comment = fstring.substring(cstart + 1, cend); // TODO: put\r
+ // this\r
+ // somewhere ?\r
+ fstring = fstring.substring(0, cstart) + fstring.substring(cend + 1);\r
+ }\r
+ Matcher uqnodename = Pattern.compile("^([^' :;\\](),]+).*").matcher(\r
+ fstring);\r
if (uqnodename.matches()\r
&& ((uqnodename.start(1) == 0) || (fstring.charAt(uqnodename\r
.start(1) - 1) != ':'))) // JBPNote HACK!\r
"File has broken algorithm - overwritten nodename", 10, fcp, nf);\r
}\r
}\r
- \r
- Matcher nbootstrap = Pattern.compile("\\S+([0-9+]+)\\S*:").matcher(fstring);\r
\r
+ Matcher nbootstrap = Pattern.compile("\\s*([+0-9]+)\\s*:.*").matcher(\r
+ fstring);\r
\r
- if (nbootstrap.matches()\r
- && (nbootstrap.start(1) > uqnodename.end(1))) {\r
- try {\r
- bootstrap = (new Integer(nbootstrap.group(1))).intValue();\r
- HasBootstrap = true;\r
- } catch (Exception e) {\r
- Error = ErrorStringrange(Error, "Can't parse bootstrap value", 4,\r
- cp + nbootstrap.start(0), nf);\r
+ if (nbootstrap.matches()) {\r
+ if (nodename != null && nbootstrap.group(1).equals(nodename)) {\r
+ nodename = null; // empty nodename - only bootstrap value\r
+ }\r
+ if ((nodename == null || nodename.length() == 0)\r
+ || nbootstrap.start(1) >= uqnodename.end(1)) {\r
+ try {\r
+ bootstrap = (new Integer(nbootstrap.group(1))).intValue();\r
+ HasBootstrap = true;\r
+ } catch (Exception e) {\r
+ Error = ErrorStringrange(Error, "Can't parse bootstrap value", 4,\r
+ ncp + nbootstrap.start(0), nf);\r
+ }\r
}\r
}\r
\r
- Matcher ndist = Pattern.compile(\r
- ":([-0-9Ee.+]+)").matcher(fstring);\r
+ Matcher ndist = Pattern.compile(".*:([-0-9Ee.+]+)").matcher(fstring);\r
boolean nodehasdistance = false;\r
\r
if (ndist.matches()) {\r
nodehasdistance = true;\r
} catch (Exception e) {\r
Error = ErrorStringrange(Error, "Can't parse node distance value",\r
- 7, cp + ndist.start(0), nf);\r
+ 7, ncp + ndist.start(0), nf);\r
}\r
}\r
\r
c.setBootstrap((HasBootstrap) ? bootstrap : DefBootstrap);\r
if (c == realroot) {\r
RootHasDistance = nodehasdistance; // JBPNote This is really\r
- // UGLY!!! Ensure root node gets\r
- // its given distance\r
+ // UGLY!!! Ensure root node gets\r
+ // its given distance\r
}\r
} else {\r
// Find a place to put the leaf\r
}\r
}\r
}\r
-\r
- // else : We do nothing if ';' is encountered.\r
}\r
\r
// Reset new node properties to obvious fakes\r
nodename = null;\r
distance = DefDistance;\r
bootstrap = DefBootstrap;\r
-\r
- cp = fcp + 1;\r
+ }\r
+ // Advance character pointers if necessary\r
+ if (nextcp == 0) {\r
+ ncp = cp = fcp + 1;\r
+ } else {\r
+ cp = nextcp;\r
+ nextcp = 0;\r
}\r
}\r
\r
public SequenceNode getTree() {\r
return root;\r
}\r
- public uk.ac.vamsas.objects.core.Treenode[] matchTreeNodeNames(String[] names, Vobject[] boundObjects)\r
- {\r
+\r
+ public uk.ac.vamsas.objects.core.Treenode[] matchTreeNodeNames(\r
+ String[] names, Vobject[] boundObjects) {\r
// todo!\r
- // also - need to reconstruct a names object id mapping (or BInaryNode) mapping for the parsed tree file\r
+ // also - need to reconstruct a names object id mapping (or BInaryNode)\r
+ // mapping for the parsed tree file\r
return null;\r
}\r
+\r
/**\r
* Generate a newick format tree according to internal flags for bootstraps,\r
* distances and root distances.\r
*/\r
private String nodeName(String name) {\r
if (NodeSafeName[0].matcher(name).find()) {\r
- return QuoteChar + NodeSafeName[1].matcher(name).replaceAll("''") + QuoteChar; // quite \r
+ return QuoteChar + NodeSafeName[1].matcher(name).replaceAll("''")\r
+ + QuoteChar; // quite\r
} else {\r
return NodeSafeName[2].matcher(name).replaceAll("_"); // whitespace\r
}\r
* @return DOCUMENT ME!\r
*/\r
private String printNodeField(SequenceNode c) {\r
- return //c.getNewickNodeName()\r
+ return // c.getNewickNodeName()\r
((c.getName() == null) ? "" : nodeName(c.getName()))\r
- + ((HasBootstrap) ? ((c.getBootstrap() > -1) ? (" " + c.getBootstrap())\r
- : "") : "") + ((HasDistances) ? (":" + c.dist) : "");\r
+ + ((HasBootstrap) ? ((c.getBootstrap() > -1) ? (((c.getName() == null) ? " "\r
+ : "") + c.getBootstrap())\r
+ : "")\r
+ : "") + ((HasDistances) ? (":" + c.dist) : "");\r
}\r
\r
/**\r
private String printRootField(SequenceNode root) {\r
return (printRootInfo) ? (((root.getName() == null) ? "" : nodeName(root\r
.getName()))\r
- + ((HasBootstrap) ? ((root.getBootstrap() > -1) ? (" " + root\r
- .getBootstrap()) : "") : "") + ((RootHasDistance) ? (":" + root.dist)\r
- : ""))\r
+ + ((HasBootstrap) ? ((root.getBootstrap() > -1) ? ((root.getName() != null ? " "\r
+ : "") + root.getBootstrap())\r
+ : "")\r
+ : "") + ((RootHasDistance) ? (":" + root.dist) : ""))\r
: "";\r
}\r
\r
// trf.parse();\r
System.out.println("Original file :\n");\r
\r
- System.out.println(Pattern.compile("\n+").matcher(newickfile.toString()).replaceAll("") + "\n");\r
+ System.out.println(Pattern.compile("\n+").matcher(newickfile.toString())\r
+ .replaceAll("")\r
+ + "\n");\r
\r
System.out.println("Parsed file.\n");\r
System.out.println("Default output type for original input.\n");\r
System.out.println(trf.print(false, false));\r
System.out.println("With bootstraps and with distances.\n");\r
System.out.println(trf.print(true, true));\r
+ System.out.println("leaves.\n");\r
+ Vector lvs = new Vector();\r
+ trf.findLeaves(trf.root, lvs);\r
+ Enumeration lv = lvs.elements();\r
+ while (lv.hasMoreElements()) {\r
+ BinaryNode leave = (BinaryNode) lv.nextElement();\r
+ if (leave.getName() != null) {\r
+ System.out.println("Node:'" + leave.getName() + "'");\r
+ }\r
+ }\r
} catch (java.io.IOException e) {\r
System.err.println("Exception\n" + e);\r
e.printStackTrace();\r
}\r
}\r
+\r
/**\r
* Search for leaf nodes.\r
- *\r
- * @param node root node to search from\r
- * @param leaves Vector of leaves to add leaf node objects too.\r
- *\r
+ * \r
+ * @param node\r
+ * root node to search from\r
+ * @param leaves\r
+ * Vector of leaves to add leaf node objects too.\r
+ * \r
* @return Vector of leaf nodes on binary tree\r
*/\r
- public Vector findLeaves(SequenceNode node, Vector leaves)\r
- { \r
- if (node == null)\r
- {\r
+ public Vector findLeaves(SequenceNode node, Vector leaves) {\r
+ if (node == null) {\r
return leaves;\r
}\r
\r
- if ( (node.left() == null) && (node.right() == null)) // Interior node detection\r
+ if ((node.left() == null) && (node.right() == null)) // Interior node\r
+ // detection\r
{\r
leaves.addElement(node);\r
\r
return leaves;\r
- }\r
- else\r
- {\r
-/* TODO: Identify internal nodes... if (node.isSequenceLabel())\r
- {\r
- leaves.addElement(node);\r
- }*/\r
- findLeaves( (SequenceNode) node.left(), leaves);\r
- findLeaves( (SequenceNode) node.right(), leaves);\r
+ } else {\r
+ /*\r
+ * TODO: Identify internal nodes... if (node.isSequenceLabel()) {\r
+ * leaves.addElement(node); }\r
+ */\r
+ findLeaves((SequenceNode) node.left(), leaves);\r
+ findLeaves((SequenceNode) node.right(), leaves);\r
}\r
\r
return leaves;\r
}\r
\r
/**\r
- * make tree node vector from a newick tree structure with associated vamsas objects\r
+ * make tree node vector from a newick tree structure with associated vamsas\r
+ * objects\r
+ * \r
* @param ntree\r
- * @return\r
+ * @return Treenode definitions for nodes with associated objects\r
+ */\r
+ public Treenode[] makeTreeNodes() {\r
+ return makeTreeNodes(true);\r
+ }\r
+\r
+ /**\r
+ * make treenode vector for a parsed tree with/out leaf node associations\r
+ * \r
+ * @param ignoreplaceholders\r
+ * if true means only associated nodes are returned\r
+ * @return treenode vector for associated or all leaves\r
*/\r
- public Treenode[] makeTreeNodes() { \r
+ public Treenode[] makeTreeNodes(boolean ignoreplaceholders) {\r
Vector leaves = new Vector();\r
findLeaves(root, leaves);\r
Vector tnv = new Vector();\r
Enumeration l = leaves.elements();\r
Hashtable nodespecs = new Hashtable();\r
- while (l.hasMoreElements())\r
- {\r
+ while (l.hasMoreElements()) {\r
BinaryNode tnode = (BinaryNode) l.nextElement();\r
- if (tnode instanceof SequenceNode)\r
- {\r
- if (!((SequenceNode) tnode).isPlaceholder())\r
- {\r
+ if (tnode instanceof SequenceNode) {\r
+ if (!(ignoreplaceholders && ((SequenceNode) tnode).isPlaceholder())) {\r
Object assocseq = ((SequenceNode) tnode).element();\r
- if (assocseq instanceof Vobject)\r
- {\r
+ if (assocseq instanceof Vobject) {\r
Vobject vobj = (Vobject) assocseq;\r
- if (vobj!=null)\r
- {\r
+ if (vobj != null) {\r
Treenode node = new Treenode();\r
node.setNodespec(makeNodeSpec(nodespecs, tnode));\r
node.setName(tnode.getName());\r
vr.addRefs(vobj);\r
node.addVref(vr);\r
tnv.addElement(node);\r
- }\r
- else\r
- {\r
- System.err.println("WARNING: Unassociated treeNode "+tnode.element().toString()+" "\r
- +((tnode.getName()!=null) ? " label "+tnode.getName() : ""));\r
+ } else {\r
+ System.err.println("WARNING: Unassociated treeNode "\r
+ + tnode.element().toString()\r
+ + " "\r
+ + ((tnode.getName() != null) ? " label " + tnode.getName()\r
+ : ""));\r
}\r
}\r
}\r
}\r
}\r
- if (tnv.size()>0)\r
- {\r
+ if (tnv.size() > 0) {\r
Treenode[] tn = new Treenode[tnv.size()];\r
- tnv.copyInto(tn); \r
+ tnv.copyInto(tn);\r
return tn;\r
}\r
return new Treenode[] {};\r
}\r
- private String makeNodeSpec(Hashtable nodespecs, BinaryNode tnode)\r
- { \r
+\r
+ private String makeNodeSpec(Hashtable nodespecs, BinaryNode tnode) {\r
String nname = new String(tnode.getName());\r
Integer nindx = (Integer) nodespecs.get(nname);\r
- if (nindx==null)\r
- {\r
+ if (nindx == null) {\r
nindx = new Integer(1);\r
}\r
- nname = nindx.toString()+" "+nname;\r
+ nname = nindx.toString() + " " + nname;\r
return nname;\r
}\r
+\r
/**\r
* call to match up Treenode specs to NJTree parsed from document object.\r
* \r
* as returned from NJTree.findLeaves( .., ..) ..\r
* @return\r
*/\r
- private BinaryNode findNodeSpec(String nodespec, Vector leaves)\r
- {\r
- int occurence=-1;\r
- String nspec = nodespec.substring(nodespec.indexOf(' ')+1);\r
+ private BinaryNode findNodeSpec(String nodespec, Vector leaves) {\r
+ int occurence = -1;\r
+ String nspec = nodespec.substring(nodespec.indexOf(' ') + 1);\r
String oval = nodespec.substring(0, nodespec.indexOf(' '));\r
try {\r
occurence = new Integer(oval).intValue();\r
- }\r
- catch (Exception e)\r
- {\r
- System.err.println("Invalid nodespec '"+nodespec+"'");\r
+ } catch (Exception e) {\r
+ System.err.println("Invalid nodespec '" + nodespec + "'");\r
return null;\r
}\r
BinaryNode bn = null;\r
- \r
+\r
int nocc = 0;\r
Enumeration en = leaves.elements();\r
- while (en.hasMoreElements() && nocc<occurence)\r
- {\r
+ while (en.hasMoreElements() && nocc < occurence) {\r
bn = (BinaryNode) en.nextElement();\r
- if (bn instanceof SequenceNode && bn.getName().equals(nspec))\r
- {\r
- --occurence;\r
- } else \r
- bn=null;\r
+ if (bn instanceof SequenceNode && bn.getName().equals(nspec)) {\r
+ --occurence;\r
+ } else\r
+ bn = null;\r
}\r
return bn;\r
}\r
+\r
/**\r
- *\r
- * re-decorate the newick node representation with the VorbaId of an object mapped by its corresponding TreeNode. \r
- * Note: this only takes the first object in the first set of references.\r
+ * \r
+ * re-decorate the newick node representation with the VorbaId of an object\r
+ * mapped by its corresponding TreeNode. Note: this only takes the first\r
+ * object in the first set of references.\r
+ * \r
* @param tn\r
- * @return vector of mappings { treenode, SequenceNode, Vobject for VorbaId on sequence node }\r
+ * @return vector of mappings { treenode, SequenceNode, Vobject for VorbaId on\r
+ * sequence node }\r
*/\r
- public Vector attachTreeMap(Treenode[] tn)\r
- {\r
- if (root!=null || tn==null)\r
- return null;\r
- Vector leaves = new Vector();\r
- Vector nodemap=new Vector();\r
- findLeaves(root, leaves);\r
- int sz = tn.length;\r
- int i = 0;\r
- \r
- while (i < sz)\r
- {\r
- Treenode node = tn[i++];\r
- BinaryNode mappednode = findNodeSpec(node.getNodespec(),leaves);\r
- if (mappednode!=null && mappednode instanceof SequenceNode) {\r
- SequenceNode leaf = (SequenceNode) leaves.elementAt(i++);\r
- // check if we can make the specified association\r
- Vobject noderef = null;\r
- int vrf=0,refv=0;\r
- while (noderef==null && vrf<node.getVrefCount())\r
- {\r
- if (refv<node.getVref(vrf).getRefsCount())\r
- {\r
- Object ref = node.getVref(vrf).getRefs(refv++);\r
- if (ref instanceof Vobject)\r
- {\r
- noderef = (Vobject) ref;\r
+ public Vector attachTreeMap(Treenode[] tn) {\r
+ if (root != null || tn == null)\r
+ return null;\r
+ Vector leaves = new Vector();\r
+ Vector nodemap = new Vector();\r
+ findLeaves(root, leaves);\r
+ int sz = tn.length;\r
+ int i = 0;\r
+\r
+ while (i < sz) {\r
+ Treenode node = tn[i++];\r
+ BinaryNode mappednode = findNodeSpec(node.getNodespec(), leaves);\r
+ if (mappednode != null && mappednode instanceof SequenceNode) {\r
+ SequenceNode leaf = (SequenceNode) leaves.elementAt(i++);\r
+ // check if we can make the specified association\r
+ Vobject noderef = null;\r
+ int vrf = 0, refv = 0;\r
+ while (noderef == null && vrf < node.getVrefCount()) {\r
+ if (refv < node.getVref(vrf).getRefsCount()) {\r
+ Object ref = node.getVref(vrf).getRefs(refv++);\r
+ if (ref instanceof Vobject) {\r
+ noderef = (Vobject) ref;\r
+ }\r
+ } else {\r
+ refv = 0;\r
+ vrf++;\r
}\r
+ }\r
+ if (noderef != null) {\r
+ nodemap.addElement(new Object[] { node, leaf, noderef });\r
+ leaf.setElement(noderef);\r
+ leaf.setPlaceholder(false);\r
} else {\r
- refv=0;\r
- vrf++;\r
+ leaf.setPlaceholder(true);\r
}\r
}\r
- if (noderef!=null)\r
- {\r
- nodemap.addElement(new Object[] { node, leaf, noderef });\r
- leaf.setElement(noderef);\r
- leaf.setPlaceholder(false);\r
- } else {\r
- leaf.setPlaceholder(true);\r
- }\r
}\r
+ return nodemap;\r
}\r
- return nodemap;\r
-}\r
\r
}\r
git://source.jalview.org / vamsas.git / blobdiff