[Biojava-dev] [biojava-builder] BioJava nightly build report
autobuilder at derkholm.net
autobuilder at derkholm.net
Thu Aug 21 03:28:34 EDT 2003
BioJava automatic build system, run 20030821
This is an experimental system, contact Thomas Down if you see any problems.
Binary build: OK
Javadocs build: OK
Core test suite: OK (results attached)
A snapshot release has been made at:
http://www.derkholm.net/autobuild/
The following files were modified in the last 24 hours:
* biojava-live/src/org/biojava/bio/MergeAnnotation.java
* biojava-live/src/org/biojava/bio/symbol/UkkonenSuffixTree.java
* biojava-live/tests/org/biojava/bio/MergeAnnotationTest.java
* biojava-live/tests/org/biojava/bio/symbol/UkkonenSuffixTreeTest.java
A patch file reflecting these changes is attached.
-------------- next part --------------
Index: biojava-live/src/org/biojava/bio/MergeAnnotation.java
diff -u biojava-live/src/org/biojava/bio/MergeAnnotation.java:1.9 biojava-live/src/org/biojava/bio/MergeAnnotation.java:1.10
--- biojava-live/src/org/biojava/bio/MergeAnnotation.java:1.9 Wed Jul 16 12:01:10 2003
+++ biojava-live/src/org/biojava/bio/MergeAnnotation.java Wed Aug 20 17:49:15 2003
@@ -25,6 +25,7 @@
import java.util.AbstractMap;
import java.util.AbstractSet;
import java.util.ArrayList;
+import java.util.Collections;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
@@ -43,12 +44,15 @@
/**
* Merged view onto a list of underlying Annotation objects.
* Currently immutable (but reflects changes to underlying objects). Annotations
- * near the beginning of the list will have properties that take precedence.
+ * near the beginning of the list will have properties that take
+ * precedence. It is possible to get the ordering of the annotations, or to
+ * change it by removing and re-adding methods.
* This Annotation implementation is immutable.
*
* @author Thomas Down
* @author Matthew Pocock
* @author Greg Cox
+ * @author Francois Pepin
* @since 1.2
*
* @for.developer Use these when you have a list of Annotation instances that
@@ -71,8 +75,45 @@
mergeSet = new ArrayList();
}
+ /**
+ * ChangeType of ChangeEvent fired before and after an annotation is added
+ * to MergeAnnotation.
+ *
+ */
+ public static final ChangeType ANNOTATION_CHANGED = new ChangeType(
+ "annotation added",
+ "org.biojava.bio.MergeAnnotation",
+ "ANNOTATION_CHANGED"
+ );
+
+ /**
+ * ChangeType of ChangeEvent fired before and after an annotation is added
+ * to MergeAnnotation.
+ *
+ */
+ public static final ChangeType ANNOTATION_ADD = new ChangeType(
+ "annotation added from List",
+ "org.biojava.bio.MergeAnnotation",
+ "ANNOTATION_ADD",
+ ANNOTATION_CHANGED
+ );
+
+ /**
+ * ChangeType of ChangeEvent fired before and after an annotation is added
+ * to MergeAnnotation.
+ *
+ */
+ public static final ChangeType ANNOTATION_REMOVE = new ChangeType(
+ "annotation deleted from List",
+ "org.biojava.bio.MergeAnnotation",
+ "ANNOTATION_REMOVE",
+ ANNOTATION_CHANGED
+ );
+
+
+
/**
- * Add a new Annotation to the list to be merged.
+ * Add a new Annotation to to the end of the list to be merged.
*
* @for.powerUser Use this to alter the Annotations being merged
*
@@ -81,9 +122,55 @@
*/
public void addAnnotation(Annotation ann)
throws ChangeVetoException {
- mergeSet.add(ann);
+ if(!hasListeners())
+ mergeSet.add(ann);
+ else{
+ ChangeEvent ce = new ChangeEvent(this,MergeAnnotation.ANNOTATION_ADD,ann);
+ ChangeSupport changeSupport = super.getChangeSupport(MergeAnnotation.ANNOTATION_ADD);
+ synchronized(changeSupport) {
+ changeSupport.firePreChangeEvent(ce);
+ mergeSet.add(ann);
+ changeSupport.firePostChangeEvent(ce);
+ }
+ }
}
+ /**
+ * Gets an unmodifiable view of the list of Annotations that are part of the
+ * MergeAnnotation. Lower indices Annotation have precedence if 2
+ * Annotations share the same property.
+ *
+ * @return an unmodifiable <code>List</code> of the Annotations that form
+ * this MergeAnnotation.
+ */
+ public List getAnnotations()
+ {
+ return Collections.unmodifiableList(mergeSet);
+ }
+
+ /**
+ * Remove an Annotation from the list. This can be used to change the
+ * ordering of the Annotations by re-adding it later.
+ *
+ * @param ann an <code>Annotation</code> to be removed.
+ * @exception ChangeVetoException if an error occurs
+ */
+ public void removeAnnotation(Annotation ann)
+ throws ChangeVetoException {
+ if(!hasListeners())
+ mergeSet.remove(ann);
+ else{
+ ChangeEvent ce = new ChangeEvent(this,MergeAnnotation.ANNOTATION_REMOVE,ann);
+ ChangeSupport changeSupport = super.getChangeSupport(MergeAnnotation.ANNOTATION_REMOVE);
+ synchronized(changeSupport) {
+ changeSupport.firePreChangeEvent(ce);
+ mergeSet.remove(ann);
+ changeSupport.firePostChangeEvent(ce);
+ }
+ }
+ }
+
+
protected ChangeSupport getChangeSupport(ChangeType changeType) {
ChangeSupport changeSupport = super.getChangeSupport(changeType);
@@ -139,7 +226,7 @@
Set s = new HashSet();
for (Iterator i = mergeSet.iterator(); i.hasNext();) {
Annotation a = (Annotation) i.next();
- s.add(a.keys());
+ s.addAll(a.keys());
}
return s;
}
Index: biojava-live/src/org/biojava/bio/symbol/UkkonenSuffixTree.java
diff -u biojava-live/src/org/biojava/bio/symbol/UkkonenSuffixTree.java:1.6 biojava-live/src/org/biojava/bio/symbol/UkkonenSuffixTree.java:1.8
--- biojava-live/src/org/biojava/bio/symbol/UkkonenSuffixTree.java:1.6 Tue Jul 29 00:57:48 2003
+++ biojava-live/src/org/biojava/bio/symbol/UkkonenSuffixTree.java Wed Aug 20 15:56:54 2003
@@ -1,10 +1,30 @@
package org.biojava.bio.symbol;
+import java.io.Serializable;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
+import java.util.List;
+import java.util.Set;
+import org.biojava.bio.Annotation;
+import org.biojava.bio.BioRuntimeException;
+import org.biojava.bio.BioError;
import org.biojava.bio.BioException;
import org.biojava.bio.seq.io.SymbolTokenization;
+import org.biojava.bio.seq.io.CharacterTokenization;
+import org.biojava.bio.seq.io.SymbolListCharSequence;
+import org.biojava.bio.symbol.IllegalAlphabetException;
+import org.biojava.bio.symbol.Alphabet;
+import org.biojava.bio.symbol.Edit;
+import org.biojava.bio.symbol.SymbolList;
+import org.biojava.bio.symbol.Symbol;
+import org.biojava.utils.Changeable;
+import org.biojava.utils.AssertionFailure;
+import org.biojava.utils.ChangeListener;
+import org.biojava.utils.ChangeType;
+import org.biojava.utils.ChangeVetoException;
+import org.biojava.utils.Unchangeable;
+
/**
* <p>
@@ -32,7 +52,7 @@
* biojava-dev at biojava.org and I'll add it in there.
*<\p>
* @author Francois Pepin
- * @version $Revision: 1.6 $
+ * @version 1.3
*/
public class UkkonenSuffixTree{
@@ -44,7 +64,7 @@
public static final int TO_A_LEAF = -1;
private int e;
- private String sequences;
+ private CharSequence sequences;
private FiniteAlphabet alpha;
@@ -64,7 +84,7 @@
*/
public UkkonenSuffixTree(){
terminationChar = DEFAULT_TERM_CHAR;
- root = new SuffixNode();
+ root = new SimpleNode();
e=0;
sequences = "";
alpha=null;
@@ -80,45 +100,15 @@
this.alpha=alpha;
}
-
- /** Makes a string out of a SymbolList, this string should only be used for
- * internal or testing purposes, as it will necessarily consist of visible
- * characters. It basically works by assigning a given character to every symbol.
- * @param list a <code>SymbolList</code> to be converted to a string.
- * @return a <code>String</code> representation of the SymbolList
- * @exception IllegalSymbolException if an error occurs
- */
- public String symbolListToString(SymbolList list) throws IllegalSymbolException{
- try {
- FiniteAlphabet alpha = (FiniteAlphabet)list.getAlphabet();
- SymbolTokenization tok = alpha.getTokenization("token");
- return tok.tokenizeSymbolList(list);
- } catch (BioException be) {
- throw new IllegalSymbolException(be.toString());
- }
- }
-
- /** Converts a string that came from symbolListToString back to a SymbolList.
- * This should only be called for internal or testing purposes. The behavior
- * is not defined if the string contains an unknown character.
- * @param string a <code>String</code> to be converted to SymbolList
- * @return a <code>SymbolList</code> representation of the string above.
- */
- public SymbolList stringToSymbolList(String string){
- try {
- SymbolTokenization tok = alpha.getTokenization("token");
- return new SimpleSymbolList(tok, string);
- } catch (BioException be) {
- System.err.println("No alphabet known to the SuffixTree.");
- return null;
- }
- }
-
public void addSymbolList(SymbolList list, String name, boolean doNotTerminate) throws IllegalSymbolException{
- String seq = symbolListToString(list);
+ if (!doNotTerminate)
+ list = new TerminatedSymbolList(list);
- if(!doNotTerminate)
- seq = seq+terminationChar;
+ CharSequence seq =new SymbolListCharSequence(list);
+ //if (!doNotTerminate)
+
+ //if(!doNotTerminate)
+ // seq = seq+terminationChar;
addPreppedSequence(seq);
}
@@ -163,7 +153,7 @@
*
* @param seq a <code>String</code> value
*/
- private void addPreppedSequence(String seq){
+ private void addPreppedSequence(CharSequence seq){
int i, gammaStart;
int j=0;
SuffixNode oldNode=null, newNode;
@@ -261,7 +251,7 @@
public SuffixNode walkTo(SuffixNode starting, String source, int from, int to){
SuffixNode currentNode;
SuffixNode arrivedAt;
- String edgeLabel;
+ CharSequence edgeLabel;
currentNode=starting;
@@ -285,12 +275,12 @@
else
rule=5;
}
- if (edgeLabel.substring(0, to-from).equals(source.substring(from,to)))
+ if (edgeLabel.subSequence(0, to-from).equals(source.substring(from,to)))
rule=4;
else
rule=3;
from=to;
- } else if (source.substring(from,from+edgeLabel.length())
+ } else if (source.subSequence(from,from+edgeLabel.length())
.equals(edgeLabel)) {
from+=edgeLabel.length();
currentNode=arrivedAt;
@@ -325,7 +315,7 @@
* stopped inside an edge. (check the rule variable to see where it
* stopped).
*/
- public SuffixNode jumpTo(SuffixNode starting, String source, int from, int to){
+ public SuffixNode jumpTo(SuffixNode starting, CharSequence source, int from, int to){
SuffixNode currentNode;
SuffixNode arrivedAt;
boolean canGoDown = true;
@@ -351,7 +341,7 @@
// System.out.println(to+" here to "+source.substring(from, to)+" "+(i++));
if (currentNode.isTerminal()){
- System.out.println("ARRGH! at "+source.substring(original, to)+
+ System.out.println("ARRGH! at "+source.subSequence(original, to)+
"("+from+","+original+","+to+
") from "+getLabel(originalNode));
//Something truly awful happened if this line is ever reached.
@@ -418,8 +408,8 @@
return childLength-parentLength;
}
- protected String getEdgeLabel(SuffixNode child){
- return sequences.substring(
+ protected CharSequence getEdgeLabel(SuffixNode child){
+ return sequences.subSequence(
child.labelStart+
(getPathLength(child)-getEdgeLength(child)),
(child.labelEnd==TO_A_LEAF)?
@@ -435,11 +425,11 @@
return node.labelEnd==TO_A_LEAF?e:node.labelEnd;
}
- protected String getLabel(SuffixNode node){
+ protected CharSequence getLabel(SuffixNode node){
if (node==root)
return "root";
else
- return sequences.substring(
+ return sequences.subSequence(
node.labelStart,
(node.labelEnd==TO_A_LEAF)?e:node.labelEnd).toString();
}
@@ -497,7 +487,7 @@
private void doRule2(SuffixNode parent, int splittingPos, int suffixStart){
//int number = getAllNodes(root, null, false).size();
- SuffixNode leaf = new SuffixNode (parent, suffixStart);
+ SuffixNode leaf = new SimpleNode (parent, suffixStart);
parent.children.put(new Character(sequences.charAt(splittingPos)), leaf);
//System.out.println("rule 2: "+sequences.charAt(splittingPos)+" from "+getLabel(parent)+ " to "+getLabel(leaf));
@@ -510,7 +500,7 @@
// suffixStart);
//int number = getAllNodes(root, null, false).size();
SuffixNode parent = child.parent;
- SuffixNode middle= new SuffixNode(parent,suffixStart,splittingPos);
+ SuffixNode middle= new SimpleNode(parent,suffixStart,splittingPos);
Character x=new Character(
sequences.charAt(child.labelStart+getPathLength(child)-getEdgeLength(child)));
@@ -546,17 +536,68 @@
* end Tree modification methods
******************************************************************/
- class SuffixNode {
+ public static abstract class SuffixNode {
+
static final int A_LEAF=-1;
SuffixNode parent;
SuffixNode suffixLink;
int labelStart, labelEnd;
HashMap children;
int[] additionalLabels;
+
+ /**
+ * Determine is this node is terminal (has no children).
+ *<p>
+ * Note that this only happens at the terminated node (if the sequences
+ * have been terminated.
+ *
+ * @return <code>true</code> if and only if this node has no children.
+ */
+
+ abstract public boolean isTerminal();
+
+ /**
+ * Determine if this node has a child corresponding to a given character
+ *
+ * @param i the first <code>Character</code> of the edge coming down this node.
+ * @return <code>true</code> if the node has a child going down from that character,
+ * false otherwise
+ */
+ abstract public boolean hasChild(Character i);
+
+ /** Gets the child of of a node that is coming down from that particular
+ * node. It returns null if no child exists or if no child exists starting
+ * on that particular character.
+ *
+ * @param i the first <code>Character</code> of the edge coming down this node
+ * @return the appropriate child <code>SuffixNode</code>, or null if it
+ * doesn't exists.
+ */
+ abstract SuffixNode getChild(Character i);
+ //abstract void addChild(SuffixTree tree, int i, SuffixNode n);
+
+ /**
+ * Returns the parent of this node, null if it's the root.
+ *
+ * @return the parent of this node, null if it's the root.
+ */
+ abstract SuffixNode getParent();
+
+ }
+
+
+ class SimpleNode extends SuffixNode{
+
+ //static final int A_LEAF=-1;
+ //SuffixNode parent;
+ //SuffixNode suffixLink;
+ //int labelStart, labelEnd;
+ //HashMap children;
+ //int[] additionalLabels;
/** Creates a root
*/
- public SuffixNode(){
+ public SimpleNode(){
parent=null;
suffixLink=null;
labelStart=0;
@@ -569,7 +610,7 @@
* @param parent the parent node
* @param position the starting value of the suffix
*/
- public SuffixNode(SuffixNode parent, int position){
+ public SimpleNode(SuffixNode parent, int position){
this();
this.parent=parent;
labelStart=position;
@@ -583,7 +624,7 @@
* @param labelStart the starting point of the path label
* @param labelStop the ending point of the path label
*/
- public SuffixNode(SuffixNode parent, int labelStart, int labelStop){
+ public SimpleNode(SuffixNode parent, int labelStart, int labelStop){
this();
this.parent=parent;
this.labelStart=labelStart;
@@ -593,6 +634,11 @@
public boolean isTerminal(){return children==null;}
+ public boolean hasChild(Character x){return getChild(x)==null;}
+ public SuffixNode getChild(Character x){
+ return (children==null)?null:(SuffixNode)children.get(x);
+ }
+ public SuffixNode getParent(){return parent;}
}
/** This is simply a debugging method to check that a node was created
@@ -603,13 +649,13 @@
*/
private void checkParent(SuffixNode child){
SuffixNode parent=child.parent;
- String parentLabel=getLabel(parent);
- String label =getLabel(child);
+ CharSequence parentLabel=getLabel(parent);
+ CharSequence label =getLabel(child);
if (parentLabel.equals("root"))
parentLabel="";
- if (parentLabel.length()>=label.length()||!parentLabel.equals(label.substring(0,parentLabel.length())))
+ if (parentLabel.length()>=label.length()||!parentLabel.equals(label.subSequence(0,parentLabel.length())))
{
System.err.println("bad addition on rule "+rule);
System.err.println(parentLabel+" against "+ label);
@@ -624,5 +670,153 @@
walkTo(root, str, 0, str.length());
return (rule==1||rule==4||rule==5);
}
-
+
+ /**
+ * Stupid little wrapper to put a termination symbol at the end. A sublist
+ * that doesn't include the termination symbol will have the same alphabet as
+ * the original, one that does will have an alphabet that includes the
+ * termination symbol.
+ *
+ */
+ private class TerminatedSymbolList implements SymbolList
+ {
+ private SymbolList unterminated;
+ final Symbol TERMINATION_SYMBOL;
+ private AbstractAlphabet alpha;
+
+ public TerminatedSymbolList(SymbolList unterminated)
+ {
+ this.unterminated=unterminated;
+ TERMINATION_SYMBOL = AlphabetManager.createSymbol("Termination");
+ FiniteAlphabet oldAlphabet = (FiniteAlphabet)unterminated.getAlphabet();
+ Set set=AlphabetManager.getAllSymbols(oldAlphabet);
+ set.add(TERMINATION_SYMBOL);
+ alpha = new SimpleAlphabet(set);
+ CharacterTokenization tokenizer =new CharacterTokenization(alpha, true);
+ tokenizer.bindSymbol(TERMINATION_SYMBOL, DEFAULT_TERM_CHAR);
+ SymbolTokenization sToke;
+ try{
+ sToke = oldAlphabet.getTokenization("token");
+ }
+ catch (BioException be){
+ throw new BioError("Internal error: failed to get SymbolTokenization for SymbolList alphabet", be);
+ }
+ if (sToke.getTokenType() != SymbolTokenization.CHARACTER)
+ throw new IllegalArgumentException("Only FiniteAlphabets using a char token are supported by UkkonenSuffixTree");
+ try{
+ for (Iterator i= AlphabetManager.getAllSymbols(oldAlphabet).iterator();i.hasNext();){
+ Symbol s = (Symbol) i.next();
+ //takes first char of String, should work because we checked
+ //getTokenType above
+ tokenizer.bindSymbol(s,sToke.tokenizeSymbol(s).charAt(0));
+ }
+ //This is really hacky, ambiguous symbols containing
+ //TERMINATION_SYMBOL are impossible at this point, so I just define
+ //the Tokenization to treat them as TERMINATION_SYMBOL so that the
+ //code that likes to loop through doesn't go titty up.
+ for (Iterator i= AlphabetManager.getAllSymbols(alpha).iterator();i.hasNext();){
+ Symbol s = (Symbol) i.next();
+ Alphabet mathes = s.getMatches();
+ if (mathes.contains(TERMINATION_SYMBOL))
+ tokenizer.bindSymbol(s,DEFAULT_TERM_CHAR);
+ }
+
+ }catch(IllegalSymbolException ise){
+ throw new AssertionFailure("Assertion Failure: This alphabet has been custom made so this doesn't happen",ise);
+ }
+
+ alpha.putTokenization("token", tokenizer);
+ }
+
+
+ // Implementation of org.biojava.utils.Changeable
+
+ public void addChangeListener(ChangeListener changeListener, ChangeType changeType) {
+ unterminated.addChangeListener(changeListener,changeType);
+ }
+
+ public void addChangeListener(ChangeListener changeListener) {
+ unterminated.addChangeListener(changeListener);
+ }
+
+ public void removeChangeListener(ChangeListener changeListener, ChangeType changeType) {
+ unterminated.removeChangeListener(changeListener,changeType);
+ }
+
+ public void removeChangeListener(ChangeListener changeListener) {
+ unterminated.removeChangeListener(changeListener);
+ }
+
+ public boolean isUnchanging(ChangeType changeType) {
+ return unterminated.isUnchanging(changeType);
+ }
+
+ // Implementation of org.biojava.bio.symbol.SymbolList
+
+ public int length() {
+ return unterminated.length()+1;
+ }
+
+ public Iterator iterator() {
+ return unterminated.iterator();
+ }
+
+ public SymbolList subList(int n, int n1) throws IndexOutOfBoundsException {
+ List list;
+ if (n1!=unterminated.length()+1)
+ return unterminated.subList(n,n1);
+ else{
+ list = unterminated.subList(n,n1-1).toList();
+ list.add(TERMINATION_SYMBOL);
+ try{
+ return new SimpleSymbolList(getAlphabet(),list);
+ }
+ catch(IllegalSymbolException e){
+ throw new AssertionFailure("Assertion Failure: This alphabet was created just so it doesn't do this",e);
+ }
+ }
+ }
+
+ public Alphabet getAlphabet() {
+ return alpha;
+ }
+
+ public Symbol symbolAt(int n) throws IndexOutOfBoundsException {
+ if (n!=length())
+ return unterminated.symbolAt(n);
+ else
+ return TERMINATION_SYMBOL;
+ }
+
+ public List toList() {
+ List answer = unterminated.toList();
+ answer.add(TERMINATION_SYMBOL);
+ return answer;
+ }
+
+ public String seqString() {
+ try{
+ SymbolTokenization toke = getAlphabet().getTokenization("token");
+ return unterminated.seqString()+toke.tokenizeSymbol(TERMINATION_SYMBOL);
+ } catch (BioException ex) {
+ throw new BioRuntimeException("Couldn't tokenize sequence", ex);
+ }
+ }
+
+ public String subStr(int n, int n1) throws IndexOutOfBoundsException {
+ return subList(n, n1).seqString();
+ }
+
+ /**
+ * Describe <code>edit</code> method here.
+ *
+ * @param edit an <code>Edit</code> value
+ * @exception IndexOutOfBoundsException if an error occurs
+ * @exception IllegalAlphabetException if an error occurs
+ * @exception ChangeVetoException if an error occurs
+ */
+ public void edit(Edit edit) throws IndexOutOfBoundsException, IllegalAlphabetException, ChangeVetoException {
+ throw new ChangeVetoException("TerminatedSymbolList is immutable");
+ }
+ }
}
Index: biojava-live/tests/org/biojava/bio/MergeAnnotationTest.java
diff -u /dev/null biojava-live/tests/org/biojava/bio/MergeAnnotationTest.java:1.1
--- /dev/null Thu Aug 21 03:27:51 2003
+++ biojava-live/tests/org/biojava/bio/MergeAnnotationTest.java Wed Aug 20 17:49:49 2003
@@ -0,0 +1,72 @@
+/*
+ * BioJava development code
+ *
+ * This code may be freely distributed and modified under the
+ * terms of the GNU Lesser General Public Licence. This should
+ * be distributed with the code. If you do not have a copy,
+ * see:
+ *
+ * http://www.gnu.org/copyleft/lesser.html
+ *
+ * Copyright for this code is held jointly by the individual
+ * authors. These should be listed in @author doc comments.
+ *
+ * For more information on the BioJava project and its aims,
+ * or to join the biojava-l mailing list, visit the home page
+ * at:
+ *
+ * http://www.biojava.org/
+ */
+
+
+package org.biojava.bio;
+
+
+import org.biojava.bio.*;
+import junit.framework.*;
+import java.util.*;
+
+/** List of tests for for MergeAnnotationTree.
+ * @author Francois Pepin
+ * @version 1.4
+ */
+public class MergeAnnotationTest extends TestCase {
+
+ Annotation anno1;
+ Annotation anno2;
+
+ MergeAnnotation merged;
+
+ public static void main(String args[]){
+ junit.textui.TestRunner.run(new TestSuite(MergeAnnotationTest.class));
+ }
+
+ protected void setUp() throws Exception
+ {
+ anno1 = new SimpleAnnotation();
+ anno1.setProperty("name", "michelle");
+ anno1.setProperty("age", "27");
+
+ anno2 = new SmallAnnotation();
+ anno2.setProperty("work", "mcb");
+ anno2.setProperty("favorite food", "?");
+ anno2.setProperty("cat", "bretelle&trouser");
+
+ merged = new MergeAnnotation();
+ merged.addAnnotation(anno1);
+ merged.addAnnotation(anno2);
+ }
+
+ public void testAnnotation() {
+ assertEquals(2,merged.getAnnotations().size());
+ }
+
+
+ public void testKeys()
+ {
+ assertEquals(5, merged.keys().size());
+ }
+
+}
+
+
Index: biojava-live/tests/org/biojava/bio/symbol/UkkonenSuffixTreeTest.java
diff -u biojava-live/tests/org/biojava/bio/symbol/UkkonenSuffixTreeTest.java:1.4 biojava-live/tests/org/biojava/bio/symbol/UkkonenSuffixTreeTest.java:1.5
--- biojava-live/tests/org/biojava/bio/symbol/UkkonenSuffixTreeTest.java:1.4 Sun May 4 19:57:15 2003
+++ biojava-live/tests/org/biojava/bio/symbol/UkkonenSuffixTreeTest.java Wed Aug 20 15:57:38 2003
@@ -6,7 +6,7 @@
/** List of tests for for UkkonenSuffixTree.
* @author Francois Pepin
- * @version $Revision: 1.4 $
+ * @version $Revision: 1.5 $
*/
public class UkkonenSuffixTreeTest extends TestCase {
@@ -44,17 +44,17 @@
assertEquals(12,test.getAllNodes(test.getRoot(), null, true).size());
}
- public void testSymbolListConversion(){
+ /*public void testSymbolListConversion(){
SymbolList here=null;
SymbolList here2=null;
try{
here = DNATools.createDNA("taccaccagga");
test = new UkkonenSuffixTree((FiniteAlphabet)here.getAlphabet());
- here2= test.stringToSymbolList(test.symbolListToString(here));
+ //here2= test.stringToSymbolList(test.symbolListToString(here));
}catch(IllegalSymbolException e){e.printStackTrace();}
for (int i=1;i<=here.length();i++)
assertEquals(here.symbolAt(i),here2.symbolAt(i));
- }
+ }*/
// adding twice the same string should be the same
public void testDuplicateAddition(){
@@ -65,6 +65,21 @@
assertEquals(12,test.getAllNodes(test.getRoot(), null, true).size());
}
+ public void testGetterMethods()
+ {
+ SymbolList here=null;
+ try{
+ here = DNATools.createDNA("taccaccagga");
+ test = new UkkonenSuffixTree((FiniteAlphabet)here.getAlphabet());
+ test.addSymbolList(here, "name", false);
+ }catch(IllegalSymbolException e){e.printStackTrace();}
+ assertTrue(test.getRoot().getParent()==null);
+ //bad test that mixes SymbolLists and CharSequence, but it still works.
+ assertTrue(test.getRoot().hasChild(new Character('g')));
+ assertTrue(test.getRoot().getChild(new Character(UkkonenSuffixTree.DEFAULT_TERM_CHAR)).isTerminal());
+ }
+
+
public void testlongAddition(){
test.addSequence(dna, "name", false);
int before = test.getAllNodes(test.getRoot(), null, false).size();
@@ -75,7 +90,6 @@
assertEquals(before, after);
//test.printTree();
-
}
private String dna=
"GGCTCAGTCCCGACGTGGAACTCAGCAGCGGAGGCTGGACGCTTGCATGGCGCTTGAGGCAAGTTCGGGGCTCATTTTGGAAGTTTTCTTTCTAGCACAGACATCCAACTCTGCTCCTATGCCAGTCAGATAATTAAGGAATTAAGTAATAATTGTGCTCTGCAAATTATGATAGTGATCTGTATTTACTACGTGCATATATTTTGGGCCAGTGAATTTTTTTCTAAGCTAATATAGTTATTTGGACTTTTGACATGACTTTGTGTTTAATTAAAACAAAAAAAGAAATTGCAGAAGTGTTGTAAGCTTGTAAAAAAATTCAAACAATGCAGACAAATGTGTCTCGCAGTCTTCCACTCAGTATCATTTTTGTTTGTACCTTATCAGAAATGTTTCTATGTACAAGTCTTTAAAATCATTTCGAACTTGCTTTGTCCACTGAGTATATTATGGACATCTTTTCATGGCAGGACATATAGATGTGTTAATGGCATTAAAAATAAAACAAAAAACTGATTCGGCCGGGTACGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGATCGAGGAGGGAGGATCACCTGAGGTCAGGAGTTACAGACATGGAGAAACCCCGTCTCTACTAAAAATACAAAATTAGCCTGGCGTGGTGGCGCATGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGCGGAGGTTGCGGTGAGCCGAGATCGCACCGTTGCACTCCAGCCTGGGCGACAGAGCGAAACTGTCTCAAACAAACAAACAAAAAAACCTGATACATGGTATGGGAAGTACATTGTTTAAACAATGCATGGAGATTTAGGTTGTTTCCAGTTTTTACTGGCACAGATACGGCAATGAATATAATTTTATGTATACATTCATACAAATATATCGGTGGAAAATTCCTAGAAGTGGAATGGCTGGGTCAGTGGGCATTCATATTGAGAAATTGGAAGGATGTTGTCAAACTCTGCAAATCAGAGTATTTTAGTCTTAACCTCTCTTCTTCACACCCTTTTCCTTGGAAGAAAGCTAAATTTAGACTTTTAAACACAAAACTCCATTTTGAGACCCCTGAAAATCTGGGTTCAAAGTGTTTGAAAATTAAAGCAGAGGCTTTAATTTGTACTTATTTAGGTATAATTTGTACTTTAAAGTTGTTCCAGAAAACAAGGCAAATACTGAAAAGCATTTCATCTGAAGTTTCTTTCTGGTATTGAACAGAGTTGGATGGAGAGTGAATGCAGGTTACCGATGTGTTCGCAGGAACAAAACGGGAGGGAGAGTAACACAGGTGCACGGCTTCATATTGATTTATCAAAGAACTTGCTTTTGGACTGTTAAAAAATGTGTTGCACAGTTCTGACACTTTTACACAATGATGAGCTTACAAAGGGGAAAATGCTTAACATAAACATAGTTTCAAAGAAGGTAAGTCCTAGTTTTTCCACGAGCTGTTTTTTTTTTTGAGAGAGAGTAGTCCCAAAATTTCCCTATTATGTGGTTTTTCATCCAAAGTGTTGTAATCCGTGTGTTCTAACCCGCATATTACGATTACTCAAGAAATGCAAAATAGGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCAATTTGGGAGGCCGAGGCAGGTGGATCACGAGGTCAGGAGATCAAGACCATCCTAGCTAACACGGTGCAAACCCATCTACTAAAAATAAAAAATATTAGCTGGGCGTGGCGGCAGGCGCCTGTAGTCCCAACTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCTGGGAGGCGGAGCTTGCAGTGAGCCAAGATCCGGCCACTGCACTCCAGCCTGGGCGACAGAGGGAGACTCCGTCTCAAAAATAAAAATAAAAATAAAAAAAGAAAAAAGAAATGCAAAATAATGTGAACACGTCATCGAGACTGCGGTCTACAATTGTGGTTGCCATGATGGGGTGGGTCGGAAGACACCGAGGCTGCTTGAATCATGTTCCTGGCAGGTTAATTTTGTTCCTTTTAGGGCATCTAAATGTTGGAGTTGGCTTTCCTGGCAGAGAGTCCAGTTGTGAGTGGAGTATTGGGTGGAGGCCCCACCCTCCCCAGGTTTTCTGCAGCTTGTTCCTGGCTCTTCTGGGGCTTCTCTGAGGACCCCGATTGGTCCTGGGGCTTCTTTAGTGGTGGGCCTGGGCCAGTTCCTTCCGTTGCTCACCTCTCCCCGAAGCTTAAGGATAACATTTCGGGAAGATCATGAGAGAACGTGAACCAAAAAAAAAAAAAAAAATTCAGGTAGGGTGGGAGCTAAGTTAGTTTAGTATTTGGGATTTTTGTTTTGTTTTGTTTGAGACAGAGTCTCAAACAAAGACCCCGCGCCTGGCCTGGGGGTCTTTTTTTGAGTCAGCAGTTGAGTTTGAAAATCCCCTTCCTTGGAATCCGCCCAGGCTGTTTTCTCTGGTGGATGCTTATTGCCCCTGCTAACTTCAGCTGCGGTCTCTCTGCTCGCCTTGCCCTCCCCATCCTCCTTAGACCTTTTAAGCTTCACTTTCCTTTCCTTGCTGCCCCGCCTCCCTGTCTCCCCAGTGTGATCTACCCTGAAAGGCTGCTGTATTTTGTTTCCCTTTGGGACCGAGCCTGCTCAAATGATCTGCTCCATGAGGTTTTACTGCTATATCCTACTGAAGTATCTGGGAGGTCTTGGCGGAGAAGAGGACAACATCTTGGAAAATGCAGCCTGGAACCTCTCTGCTCTCTTTCATCAGCTTTCCCTCAATGATGAGCTCAAAATCCTCTTTCTTGCTGATGGAATTGTCTGCTGTCATCATTTCAGTTGAGTCCTCCTAGGCTGGGCCTTGTAAGAAGAACAACTGTTTATAACTATTGAAAGTCAATATTTACTAAGAAAAAGAGGTTGTTGTTATCTGAGCCATCCAACATGAATTTAAGAATATATTCCAGGCTGGGCGCGGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCCGAGATGGGTGGATCACCTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCATGCGTGGTGGCACATGCCTGTAGTTCCAACTATTTGGGACACTAAGGCAGGGGAAGTGCTTGAACTCGGGAGGCAGAGGTTGCAGTGAGCTGAGATTGTACCACTGCACTCCAGCCTGGGTAAAAAGAGTGAAATTCCATCTCAAAAAAAAAAAAGGAGACAGGGTCTTGCCCTGTTGCCCAGGCTGGAGTGCCGTGGCACGATCATAACTCACTGTGGCCTCAAATTCCTGGGCTCAACTGATTCTCCTGCCTCAGTCTCCCAAGTAGCTGGGACCACAAGTACATGCCACCATGCTAGGCTAATTTTATTTTTATTTTTAGAAAATAAAATATTTTTTATTTTATTTAGGCAACATGCTATGTTGCCTAGACTGGTCTTGAACTCCTGGCTTCAAGCTATCCTCTTGCCTCAGCCAACCAAAGTGCTGGGATTGCAGGTGTGAACTGCCATGCCTGGCTTTCTATTCTCTATTTCTAGGAGATAAGCTTTTTGAGCTTTCACATATGAGTGTGAACATGTGGTATTTATCTTTCTGTGCCTAGGTTATTCCACTTAACGTAATGTACTCCAGGCTCATCCATGTTGATGGGAATTACAGGATTTCATTCTCTTGTAATGGCTGAATAACATCCCATTTTGTGTATATAGTCCACATGTTCTTTATCCATTCCTCTTTTGATAGACACTTAGGTTGATTCCGTATCTCGGGTATTATGAGCAGTGCTGCAGTAAACATGAGAGTGCAAATATCTCTTCAACATACTGATTCCCTTTCCTTTGGATATATATTCAGCAGT";
-------------- next part --------------
Buildfile: build.xml
init:
[echo] JUnit present: true
[echo] JUnit supported by Ant: true
prepare:
prepare-core:
prepare-src:
compile:
package:
compile-tests:
[javac] Compiling 95 source files to /home/thomas/bjtemp/biojava-20030821/ant-build/classes/tests
[javac] depend attribute is not supported by the modern compiler
runtests:
[junit] Running org.biojava.bio.symbol.CompoundLocationTest
[junit] Tests run: 11, Failures: 0, Errors: 0, Time elapsed: 0.301 sec
[junit] Running org.biojava.bio.symbol.RangeLocationTest
[junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 0.094 sec
[junit] Running org.biojava.bio.symbol.CrossProductAlphabetIndexTest
[junit] Tests run: 4, Failures: 0, Errors: 0, Time elapsed: 38.69 sec
[junit] Running org.biojava.bio.symbol.AlphabetManagerTest
[junit] Tests run: 4, Failures: 0, Errors: 0, Time elapsed: 2.292 sec
[junit] Running org.biojava.bio.symbol.CircularLocationTest
[junit] Tests run: 9, Failures: 0, Errors: 0, Time elapsed: 0.148 sec
[junit] Running org.biojava.bio.symbol.MergeLocationTest
[junit] Tests run: 6, Failures: 0, Errors: 0, Time elapsed: 0.108 sec
[junit] Running org.biojava.bio.symbol.IntegerAlphabetTest
[junit] Tests run: 4, Failures: 0, Errors: 0, Time elapsed: 1.56 sec
[junit] Running org.biojava.bio.symbol.NameTokenizationTest
[junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 1.599 sec
[junit] Running org.biojava.bio.symbol.SymbolSerializationTest
[junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 1.717 sec
[junit] Running org.biojava.bio.symbol.UkkonenSuffixTreeTest
[junit] Tests run: 5, Failures: 0, Errors: 2, Time elapsed: 1.876 sec
[junit] Running org.biojava.bio.symbol.SimpleSymbolListTest
[junit] Tests run: 10, Failures: 0, Errors: 0, Time elapsed: 1.607 sec
[junit] Running org.biojava.bio.symbol.TranslationTest
[junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 2.841 sec
[junit] Running org.biojava.bio.symbol.SimpleWobbleDistributionTest
[junit] Tests run: 1, Failures: 0, Errors: 0, Time elapsed: 1.427 sec
[junit] Running org.biojava.bio.symbol.BetweenLocationTest
[junit] Tests run: 34, Failures: 0, Errors: 0, Time elapsed: 0.119 sec
[junit] Running org.biojava.bio.symbol.PointLocationTest
[junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 0.103 sec
[junit] Running org.biojava.bio.symbol.SimpleCodonPrefTest
[junit] Tests run: 4, Failures: 0, Errors: 0, Time elapsed: 1.447 sec
[junit] Running org.biojava.bio.symbol.PackedDnaSymbolListTest
[junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 1.674 sec
[junit] Running org.biojava.bio.symbol.CodonPrefToolsTest
[junit] Tests run: 1, Failures: 0, Errors: 0, Time elapsed: 3.425 sec
[junit] Running org.biojava.bio.symbol.MotifToolsTest
[junit] Tests run: 13, Failures: 0, Errors: 0, Time elapsed: 1.634 sec
[junit] Running org.biojava.bio.symbol.AlphabetSerializationTest
[junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 2.538 sec
[junit] Running org.biojava.bio.symbol.SymbolListTest
[junit] Tests run: 4, Failures: 0, Errors: 0, Time elapsed: 5.26 sec
[junit] Running org.biojava.bio.symbol.CrossProductTokenizationTest
[junit] Tests run: 1, Failures: 0, Errors: 0, Time elapsed: 1.611 sec
[junit] Running org.biojava.bio.symbol.GappedSymbolListTest
[junit] Tests run: 9, Failures: 0, Errors: 0, Time elapsed: 1.601 sec
[junit] Running org.biojava.bio.symbol.DoubleAlphabetTest
[junit] Tests run: 3, Failures: 0, Errors: 0, Time elapsed: 1.546 sec
[junit] Running org.biojava.bio.seq.homol.SimpleSimilarityPairFeatureTest
[junit] Tests run: 8, Failures: 0, Errors: 0, Time elapsed: 1.828 sec
[junit] Running org.biojava.bio.seq.DNAToolsTest
[junit] Tests run: 10, Failures: 0, Errors: 0, Time elapsed: 1.617 sec
[junit] Running org.biojava.bio.seq.CircularSequenceTest
[junit] Tests run: 4, Failures: 0, Errors: 0, Time elapsed: 0.277 sec
[junit] Running org.biojava.bio.seq.io.SmartSequenceBuilderTest
[junit] Tests run: 1, Failures: 0, Errors: 0, Time elapsed: 6.221 sec
[junit] Running org.biojava.bio.seq.io.SeqIOToolsTest
[junit] Tests run: 4, Failures: 0, Errors: 0, Time elapsed: 6.429 sec
[junit] Running org.biojava.bio.seq.io.agave.AGAVEHandlerTest
[junit] Tests run: 3, Failures: 0, Errors: 0, Time elapsed: 2.438 sec
[junit] Running org.biojava.bio.seq.io.MSFAlignmentFormatTest
[junit] Tests run: 1, Failures: 0, Errors: 0, Time elapsed: 1.671 sec
[junit] Running org.biojava.bio.seq.io.LocationFormatterTest
[junit] Tests run: 26, Failures: 0, Errors: 0, Time elapsed: 2.803 sec
[junit] Running org.biojava.bio.seq.io.filterxml.FilterXMLTest
[junit] Tests run: 12, Failures: 0, Errors: 0, Time elapsed: 1.433 sec
[junit] Running org.biojava.bio.seq.db.emblcd.EntryNamRandomAccessTest
[junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 0.068 sec
[junit] Running org.biojava.bio.seq.db.emblcd.DivisionLkpReaderTest
[junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 0.079 sec
[junit] Running org.biojava.bio.seq.db.emblcd.EntryNamIdxReaderTest
[junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 0.079 sec
[junit] Running org.biojava.bio.seq.db.EmblCDROMIndexStoreTest
[junit] Tests run: 11, Failures: 0, Errors: 0, Time elapsed: 2.37 sec
[junit] Running org.biojava.bio.seq.FilterUtilsTest
[junit] Tests run: 23, Failures: 0, Errors: 0, Time elapsed: 0.373 sec
[junit] Running org.biojava.bio.seq.MergeFeatureHolderTest
[junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 0.174 sec
[junit] Running org.biojava.bio.seq.FeatureFilterTest
[junit] Tests run: 8, Failures: 0, Errors: 0, Time elapsed: 2 sec
[junit] Running org.biojava.bio.seq.NewSimpleAssemblyTest
[junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 2.303 sec
[junit] Running org.biojava.bio.seq.SimpleAssemblyTest
[junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 2.372 sec
[junit] Running org.biojava.bio.seq.impl.GappedSequenceTest
[junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 2.275 sec
[junit] Running org.biojava.bio.seq.impl.ViewSeqSerializationTest
[junit] Tests run: 3, Failures: 0, Errors: 0, Time elapsed: 2.418 sec
[junit] Running org.biojava.bio.seq.impl.SubSequenceTest
[junit] Tests run: 8, Failures: 0, Errors: 0, Time elapsed: 2.456 sec
[junit] Running org.biojava.bio.seq.project.ProjectedFeatureHolderTest
[junit] Tests run: 6, Failures: 0, Errors: 0, Time elapsed: 2.325 sec
[junit] Running org.biojava.bio.seq.filter.FilterTransformerTest
[junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 0.583 sec
[junit] Running org.biojava.bio.seq.SeqSerializationTest
[junit] Tests run: 4, Failures: 0, Errors: 0, Time elapsed: 2.048 sec
[junit] Running org.biojava.bio.seq.RNAToolsTest
[junit] Tests run: 34, Failures: 0, Errors: 0, Time elapsed: 2.978 sec
[junit] Running org.biojava.bio.dp.MarkovModelEventTest
[junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 1.683 sec
[junit] Running org.biojava.bio.dp.EmissionStateEventTest
[junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 1.636 sec
[junit] Running org.biojava.bio.search.SimpleSeqSimilaritySearchResultTest
[junit] Tests run: 5, Failures: 0, Errors: 0, Time elapsed: 2.238 sec
[junit] Running org.biojava.bio.search.SimpleSeqSimilaritySearchHitTest
[junit] Tests run: 6, Failures: 0, Errors: 0, Time elapsed: 2.216 sec
[junit] Running org.biojava.bio.search.SimpleSeqSimilaritySearchSubHitTest
[junit] Tests run: 5, Failures: 0, Errors: 0, Time elapsed: 2.286 sec
[junit] Running org.biojava.bio.program.ssbind.SSBindWUblastn2_0a19Test
[junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 2.903 sec
[junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test
[junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 8.721 sec
[junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_2_3Test
[junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 5.395 sec
[junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_2_3Test
[junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 9.005 sec
[junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_2_3Test
[junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 9.282 sec
[junit] Running org.biojava.bio.program.ssbind.SSBindFasta3_3t08Test
[junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 3.433 sec
[junit] Running org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test
[junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 18.469 sec
[junit] Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_0_11Test
[junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 9.015 sec
[junit] Running org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test
[junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 3.151 sec
[junit] Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_2_3Test
[junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 9.562 sec
[junit] Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_2_3Test
[junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 30.097 sec
[junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test
[junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 5.434 sec
[junit] Running org.biojava.bio.program.ssbind.SSBindWUtblastx2_0a19Test
[junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 3.887 sec
[junit] Running org.biojava.bio.program.ssbind.SSBindWUblastp2_0a19Test
[junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 2.669 sec
[junit] Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_0_11Test
[junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 21.55 sec
[junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test
[junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 8.618 sec
[junit] Running org.biojava.bio.program.indexdb.IndexToolsTest
[junit] Tests run: 6, Failures: 0, Errors: 0, Time elapsed: 3.823 sec
[junit] Running org.biojava.bio.program.phred.PhredToolsTest
[junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 1.66 sec
[junit] Running org.biojava.bio.MergeAnnotationTest
[junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 0.087 sec
[junit] Running org.biojava.bio.AnnotationTypeTest
[junit] Tests run: 7, Failures: 0, Errors: 0, Time elapsed: 0.174 sec
[junit] Running org.biojava.bio.molbio.RestrictionEnzymeManagerTest
[junit] Tests run: 5, Failures: 0, Errors: 0, Time elapsed: 2.003 sec
[junit] Running org.biojava.bio.molbio.RestrictionEnzymeTest
[junit] Tests run: 8, Failures: 0, Errors: 0, Time elapsed: 1.954 sec
[junit] Running org.biojava.bio.dist.DistSerTest
[junit] Tests run: 4, Failures: 0, Errors: 0, Time elapsed: 2.38 sec
[junit] Running org.biojava.bio.dist.DistributionToolsTest
[junit] Tests run: 3, Failures: 0, Errors: 0, Time elapsed: 2.013 sec
[junit] Running org.biojava.bio.dist.DistributionTest
[junit] Tests run: 4, Failures: 0, Errors: 0, Time elapsed: 1.753 sec
[junit] Running org.biojava.bio.alignment.FlexibleAlignmentTest
[junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 0.026 sec
[junit] Running org.biojava.bio.proteomics.MassCalcTest
[junit] Tests run: 4, Failures: 0, Errors: 0, Time elapsed: 2.104 sec
[junit] Running org.biojava.directory.SystemRegistryTest
[junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 0.453 sec
[junit] Running org.biojava.directory.RegistryConfigurationTest
[junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 0.033 sec
[junit] Running org.biojava.directory.OBDARegistryParserTest
[junit] Tests run: 1, Failures: 0, Errors: 0, Time elapsed: 0.054 sec
[junit] Running org.biojava.ontology.TermImplTest
[junit] Tests run: 6, Failures: 0, Errors: 0, Time elapsed: 0.167 sec
[junit] Running org.biojava.ontology.OntologyTest
[junit] Tests run: 21, Failures: 0, Errors: 0, Time elapsed: 0.167 sec
[junit] Running org.biojava.ontology.ReasoningDomainTest
[junit] Tests run: 3, Failures: 0, Errors: 0, Time elapsed: 14.977 sec
[junit] Running org.biojava.ontology.TripleImplTest
[junit] Tests run: 8, Failures: 0, Errors: 0, Time elapsed: 0.138 sec
[junit] Running org.biojava.utils.ListToolsTest
[junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 0.031 sec
[junit] Running org.biojava.utils.walker.WalkerTest
[junit] Tests run: 4, Failures: 0, Errors: 0, Time elapsed: 0.485 sec
[junit] Running org.biojava.utils.walker.WalkerFactoryTest
[junit] Tests run: 4, Failures: 0, Errors: 0, Time elapsed: 0.396 sec
[junit] Running org.biojava.utils.lsid.LifeScienceIdentifierTest
[junit] Tests run: 10, Failures: 0, Errors: 0, Time elapsed: 0.125 sec
BUILD SUCCESSFUL
Total time: 6 minutes 49 seconds
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