New upstream version 1.7.8 (50db23f5) · Commits · Debian Med / logol

CHANGELOG.txt

+2 −0

Original line number	Diff line number	Diff line
		History:
		1.7.8: 03/04/18 O. Sallou - Detect process execution failure (out of memory, etc.) and display error message
		1.7.7: 08/12/17 O. Sallou - Fix not and spacer contraints when reaching end of sequence (last characters)
		1.7.6: 07/12/17 O. Sallou - Fix endConstraint, was comparing end position + 1 instead of end position
		1.7.5: 09/09/16 O. Sallou - Fix way to load characters from sequence file to increase performance
		1.7.4: 08/01/16 O. Sallou - Fix multiexec error message display

build.xml

+1 −1

Original line number	Diff line number	Diff line
		@@ -10,7 +10,7 @@
		target.dir=/path_where_files_should_be_installed
		-->

		<property name="version" value="1.7.6" />
		<property name="version" value="1.7.8" />

		<condition property="ruby_path" value="${env.RUBY_PATH}"
		else="">

prolog/logol.pl

+3 −2

Original line number	Diff line number	Diff line
		@@ -1013,7 +1013,8 @@ spacer_withresult([X\|Y],Min, Max, Word, Z) :- (((Min=0,NewX=[X\|Y]);(Min>0,cut_se
		%spacer_withresult([X\|Y],Min, Max, Z, Word) :- N is 0,((Min=0,Z=[X \| Y]);(spacer_withresult([X\|Y],N,Min,Max,Z,[], Word))).

		% sub predicate, do not call directly
		spacer_withresult([], N, Min, Max, Z, Spacer, Word) :- fail.
		%spacer_withresult([], N, Min, Max, Z, Spacer, Word) :- fail.
		spacer_withresult([], N, Min, Max, Z, Spacer, Word) :- Word=Spacer.
		% sub predicate, do not call directly
		%spacer_withresult([X\|Y],N, Min, Max, Z, Spacer, Word) :- Ninc is N+1,append(Spacer, [X], IncWord),((Ninc<Max,isalphabet(X), spacer_withresult(Y,Ninc,Min,Max,Z,IncWord, Word));(Ninc>=Min,Z = Y, Word=IncWord)).
		spacer_withresult([X\|Y],N, Min, Max, Z, Spacer, Word) :- (Z = [X \|Y], Word=Spacer); (Ninc is N+1,append(Spacer, [X], IncWord),Ninc=<Max, spacer_withresult(Y,Ninc,Min,Max,Z,IncWord, Word)).
		@@ -2459,7 +2460,7 @@ between(Min,Cur,Max,Value):-Cur=<Max,(Value=Cur;Next is Cur + 1,between(Min,Next
		% Fix 1406
		% Call predicate. If match, return last argument e.g. position, else return 0.
		callpred(Pred,OutPos,Pos):- (Pred ,(Pred=..VarDef,nth0(OutPos,VarDef,Pos)));(Pos=0).
		notpred_pos(VarId,StartPos,Pred,Min,Max,Value):-random(Id),retractall(hasmatch(Id,_)),Pred=..VarDef,length(VarDef,Predlength),OutPos is Predlength - 1,PosMin is StartPos + Min, PosMax is StartPos + Max,!,between(StartPos,PosMax,Value),(callpred(Pred,OutPos,Pos) , ((\+hasmatch(Id,Pos) -> (assert(hasmatch(Id,Pos)));1=1),\+hasmatch(Id,Value),assert(hasmatch(Id,Value)))),Value>=PosMin.
		notpred_pos(VarId,StartPos,Pred,Min,Max,OutputPos):-random(Id),retractall(hasmatch(Id,_)),Pred=..VarDef,length(VarDef,Predlength),OutPos is Predlength - 1,PosMin is StartPos + Min, PosMax is StartPos + Max,!,between(StartPos,PosMax,Value),(callpred(Pred,OutPos,Pos) , ((\+hasmatch(Id,Pos) -> (assert(hasmatch(Id,Pos)));1=1),\+hasmatch(Id,Value),assert(hasmatch(Id,Value)))),Value>=PosMin,ValueLength is Value - StartPos,getCharsFromPosition(StartPos,ValueLength,FoundWord),length(FoundWord,FoundLength),FoundLength >= Min, FoundLength=<Max, OutputPos is StartPos+FoundLength.


		% Test predicate to use with predicate requiring a position relative predicate as parameter.

src/org/irisa/genouest/logol/SequenceAnalyser.java

+64 −59

Original line number	Diff line number	Diff line
		@@ -216,6 +216,11 @@ public class SequenceAnalyser extends Thread {
		s2.start ();
		logger.debug("start program execution ");
		logol.waitFor();
		int status_code = logol.exitValue();
		if(status_code != 0){
		logger.error("Program exited with wrong status code: " + status_code);
		throw new IOException("Program exited with wrong status code");
		}

		logger.debug("program is over, results are available in file "+resultFileName);
		os.close();

src/org/irisa/genouest/logol/test/GrammarTest.java

+46 −0

Original line number	Diff line number	Diff line
		@@ -2350,6 +2350,52 @@ public class GrammarTest {
		}
		}

		@Test
		public void testEndOfStream1() {

		init();

		Vector<String[]> result = new Vector<String[]>();
		result.add(new String[] {"LogolVAR_1","32","38"});
		result.add(new String[] {"LogolVAR_2","39","40"});
		execute("test.fasta","end_of_stream1.logol");

		try {
		checkResult(result,0);
		} catch (ParserConfigurationException e) {
		fail(e.getMessage());
		} catch (SAXException e) {
		fail(e.getMessage());
		} catch (IOException e) {
		fail(e.getMessage());
		} catch (TransformerException e) {
		fail(e.getMessage());
		}
		}

		@Test
		public void testEndOfStream2() {

		init();

		Vector<String[]> result = new Vector<String[]>();
		result.add(new String[] {"LogolVAR_1","32","38"});
		result.add(new String[] {"LogolVAR_2","39","40"});
		execute("test.fasta","end_of_stream2.logol");

		try {
		checkNoMatch(result,0);
		} catch (ParserConfigurationException e) {
		fail(e.getMessage());
		} catch (SAXException e) {
		fail(e.getMessage());
		} catch (IOException e) {
		fail(e.getMessage());
		} catch (TransformerException e) {
		fail(e.getMessage());
		}
		}

		@Test
		public void testRubyCassiopee() {
		try {