public NJTree(SequenceNode node) {\r
top = node;\r
maxheight = findHeight(top);\r
-\r
}\r
- // Private SequenceID class to do fuzzy .equals() method for Hashtable.\r
-\r
- private class SeqIdname {\r
- String id;\r
-\r
- SeqIdname(String s) {\r
- id = new String(s);\r
- }\r
- public int hashCode() {\r
- return (id.substring(0,4).hashCode());\r
- }\r
- public boolean equals(Object s) {\r
- if (s instanceof SeqIdname) {\r
- return this.equals((SeqIdname) s);\r
- } else {\r
- if (s instanceof String) {\r
- return this.equals((String) s);\r
- }\r
- }\r
- return false;\r
- }\r
\r
-\r
- public boolean equals(SeqIdname s) {\r
- if (id.startsWith(s.id) || s.id.startsWith(id)) {\r
- return true;\r
- }\r
- return false;\r
- }\r
-\r
- public boolean equals(String s) {\r
- if (id.startsWith(s) || s.startsWith(id)) {\r
- return true;\r
- }\r
- return false;\r
- }\r
+ public String toString()\r
+ {\r
+ jalview.io.NewickFile fout = new jalview.io.NewickFile(getTopNode());\r
+ return fout.print(false,true); // distances only\r
}\r
\r
public NJTree(SequenceI[] seqs, NewickFile treefile) {\r
top = treefile.getTree();\r
maxheight = findHeight(top);\r
- Hashtable names = new Hashtable();\r
- for (int i = 0; i < seqs.length; i++)\r
- {\r
- names.put(new SeqIdname(seqs[i].getDisplayId()), seqs[i]);\r
- }\r
+ SequenceIdMatcher algnIds = new SequenceIdMatcher(seqs);\r
+\r
Vector leaves = new Vector();\r
findLeaves(top, leaves);\r
+\r
int i = 0;\r
int namesleft = seqs.length;\r
+\r
SequenceNode j;\r
- SeqIdname nam;\r
+ SequenceI nam;\r
+ String realnam;\r
while (i < leaves.size())\r
{\r
j = (SequenceNode) leaves.elementAt(i++);\r
- nam = new SeqIdname(j.getName());\r
- if ((namesleft>-1)\r
- && names.containsKey(nam))\r
- {\r
- j.setElement(names.get(nam));\r
+ realnam = j.getName();\r
+ nam = null;\r
+ if (namesleft>-1)\r
+ nam = algnIds.findIdMatch(realnam);\r
+ if (nam != null) {\r
+ j.setElement(nam);\r
namesleft--;\r
} else {\r
- j.setElement(new Sequence(nam.id, "THISISAPLACEHLDER"));\r
+ j.setElement(new Sequence(realnam, "THISISAPLACEHLDER"));\r
+ j.setPlaceholder(true);\r
+\r
+ }\r
+ }\r
+ }\r
+\r
+ /**\r
+ *\r
+ * used when the alignment associated to a tree has changed.\r
+ *\r
+ * @param alignment Vector\r
+ */\r
+ public void UpdatePlaceHolders(Vector alignment) {\r
+ Vector leaves = new Vector();\r
+ findLeaves(top, leaves);\r
+ int sz = leaves.size();\r
+ SequenceIdMatcher seqmatcher=null;\r
+ int i=0;\r
+ while (i<sz) {\r
+ SequenceNode leaf = (SequenceNode) leaves.elementAt(i++);\r
+ if (alignment.contains(leaf.element()))\r
+ leaf.setPlaceholder(false);\r
+ else {\r
+ if (seqmatcher==null) {\r
+ // Only create this the first time we need it\r
+ SequenceI[] seqs = new SequenceI[alignment.size()];\r
+ for (int j=0; j<seqs.length; j++)\r
+ seqs[j] = (SequenceI) alignment.elementAt(j);\r
+ seqmatcher = new SequenceIdMatcher(seqs);\r
+ }\r
+ SequenceI nam = seqmatcher.findIdMatch(leaf.getName());\r
+ if (nam!=null) {\r
+ leaf.setPlaceholder(false);\r
+ leaf.setElement(nam);\r
+ } else {\r
+ leaf.setPlaceholder(true);\r
+ }\r
}\r
}\r
}\r
if (j==i) {\r
distance[i][i] = 0;\r
} else {\r
- distance[i][j] = 100-Comparison.PID(sequence[i], sequence[j]);\r
+ distance[i][j] = 100-Comparison.PID(sequence[i], sequence[j], start, end);\r
distance[j][i] = distance[i][j];\r
}\r
}\r
for (int i = 0; i < noseqs-1; i++) {\r
for (int j = i; j < noseqs; j++) {\r
int score = 0;\r
- for (int k=0; k < sequence[i].getLength(); k++) {\r
+ for (int k=start; k < end; k++) {\r
try{\r
score +=\r
ResidueProperties.getBLOSUM62(sequence[i].getSequence(k,\r
k + 1),\r
sequence[j].getSequence(k,\r
k + 1));\r
- }catch(Exception ex){System.out.println("err creating BLOSUM62 tree");}\r
+ }catch(Exception ex){System.err.println("err creating BLOSUM62 tree");ex.printStackTrace();}\r
}\r
distance[i][j] = (float)score;\r
if (score > maxscore) {\r
return found;\r
}\r
\r
+ /**\r
+ * printNode is mainly for debugging purposes.\r
+ *\r
+ * @param node SequenceNode\r
+ */\r
public void printNode(SequenceNode node) {\r
if (node == null) {\r
return;\r
\r
float dist = ((SequenceNode)node).dist;\r
if (dist > maxDistValue) {\r
- maxdist = (SequenceNode)node;\r
- maxDistValue = dist;\r
+ maxdist = (SequenceNode)node;\r
+ maxDistValue = dist;\r
}\r
} else {\r
findMaxDist((SequenceNode)node.left());\r
}\r
}\r
public Vector getGroups() {\r
- return groups;\r
+ return groups;\r
}\r
public float getMaxHeight() {\r
- return maxheight;\r
+ return maxheight;\r
}\r
public void groupNodes(SequenceNode node, float threshold) {\r
if (node == null) {\r
}\r
\r
public void reCount(SequenceNode node) {\r
- ycount = 0;\r
- _reCount(node);\r
+ ycount = 0;\r
+ _reCount(node);\r
}\r
public void _reCount(SequenceNode node) {\r
if (node == null) {\r
\r
}\r
public void swapNodes(SequenceNode node) {\r
- if (node == null) {\r
- return;\r
- }\r
- SequenceNode tmp = (SequenceNode)node.left();\r
+ if (node == null) {\r
+ return;\r
+ }\r
+ SequenceNode tmp = (SequenceNode)node.left();\r
\r
- node.setLeft(node.right());\r
- node.setRight(tmp);\r
+ node.setLeft(node.right());\r
+ node.setRight(tmp);\r
}\r
public void changeDirection(SequenceNode node, SequenceNode dir) {\r
if (node == null) {\r
}\r
}\r
public void setMaxDist(SequenceNode node) {\r
- this.maxdist = maxdist;\r
+ this.maxdist = maxdist;\r
}\r
public SequenceNode getMaxDist() {\r
- return maxdist;\r
+ return maxdist;\r
}\r
public SequenceNode getTopNode() {\r
- return top;\r
+ return top;\r
}\r
\r
}\r
git://source.jalview.org / jalview.git / blobdiff