Merge pull request biojava#18 from andreasprlic/master

andreasprlic · andreasprlic · commit 41e044e635e6 · 2013-04-24T18:35:13.000-07:00
fixing issue biojava#12
diff --git a/biojava3-structure/src/main/java/org/biojava/bio/structure/align/xml/AFPChainXMLParser.java b/biojava3-structure/src/main/java/org/biojava/bio/structure/align/xml/AFPChainXMLParser.java
@@ -257,8 +257,7 @@ public static AFPChain[] parseMultiXML(String xml) {
 				
 				a.setAlignScore(new Double(getAttribute(rootElement,"alignScore")).doubleValue());
 				a.setChainRmsd(new Double(getAttribute(rootElement,"chainRmsd")).doubleValue());
-				Double identity = new Double(getAttribute(rootElement,"identity")).doubleValue();
-				System.out.println("parsed identity from file " + identity);
+				Double identity = new Double(getAttribute(rootElement,"identity")).doubleValue();				
 				a.setIdentity(identity);
 				
 				a.setNormAlignScore(new Double(getAttribute(rootElement,"normAlignScore")).doubleValue());
diff --git a/integrationtest/src/test/java/org/biojava/bio/structure/TestSECalignment.java b/integrationtest/src/test/java/org/biojava/bio/structure/TestSECalignment.java
diff --git a/integrationtest/src/test/java/org/biojava/bio/structure/align/FlipAFPChainTest.java b/integrationtest/src/test/java/org/biojava/bio/structure/align/FlipAFPChainTest.java
@@ -93,7 +93,7 @@ private void flip(String name1, String name2, String algorithmName) throws Struc
 		afpChain.setName1(name1);
 		afpChain.setName2(name2);
 
-
+		afpChain.setCalculationTime(0);
 
 		String xml = AFPChainXMLConverter.toXML(afpChain, ca1, ca2);
 
@@ -107,18 +107,7 @@ private void flip(String name1, String name2, String algorithmName) throws Struc
 		assertEquals(afpChain.getAlgorithmName(),flipped.getAlgorithmName());
 		assertEquals(afpChain.getVersion(), flipped.getVersion());
 
-		//System.out.println(AFPChainXMLConverter.toXML(flipped));
-
-		//AFPChainXMLParser.rebuildAFPChain(flipped, ca2, ca1);
-
-		//FatCat newCat = new FatCat();
-
-		//Group[] twistedGroups = AFPTwister.twistOptimized(flipped,ca2,ca1);
-
-		// FatCatAligner aligner =  newCat.getFatCatAligner();
-		//aligner.setTwistedGroups(twistedGroups);			
-		//newCat.display(flipped, ca2, ca1,  new ArrayList<Group>(),new ArrayList<Group>(),new ArrayList<Group>(),new ArrayList<Group>());
-
+		
 		String xmlNew = AFPChainXMLConverter.toXML(flipped, ca2, ca1);
 
 		AFPChain backChain = AFPChainXMLParser.fromXML(xmlNew, ca2, ca1);
diff --git a/integrationtest/src/test/resources/ce_1fdo.A_2iv2.X.out b/integrationtest/src/test/resources/ce_1fdo.A_2iv2.X.out
@@ -1,4 +1,4 @@
-<AFPChain name1="1FDO.A" name2="2IV2.X" method="jCE" version="1.1" alnLength="720" blockNum="1" gapLen="28" optLength="692" totalLenIni="697" alignScore="1551.34" chainRmsd="0.91" identity="0.9957" normAlignScore="0.00" probability="8.40e+00" similarity="0.9957" similarity1="97" similarity2="99" totalRmsdIni="1.36" totalRmsdOpt="0.91" ca1Length="715" ca2Length="697" afpNum="4" alignScoreUpdate="0.00" time="-1">
+<AFPChain name1="1FDO.A" name2="2IV2.X" method="jCE" version="1.1" alnLength="720" blockNum="1" gapLen="28" optLength="692" totalLenIni="697" alignScore="1551.34" chainRmsd="0.91" identity="0.9569" normAlignScore="0.00" probability="8.40e+00" similarity="0.9569" similarity1="97" similarity2="99" totalRmsdIni="1.36" totalRmsdOpt="0.91" ca1Length="715" ca2Length="697" afpNum="4" alignScoreUpdate="0.00" time="-1">
   <block blockNr="0" blockSize="0" blockScore="0.00" blockRmsd="0.91" blockGap="0">
     <eqr eqrNr="0" pdbres1="1" chain1="A" pdbres2="1" chain2="X" />
     <eqr eqrNr="1" pdbres1="2" chain1="A" pdbres2="2" chain2="X" />

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-<AFPChain name1="1FDO.A" name2="2IV2.X" method="jCE" version="1.1" alnLength="720" blockNum="1" gapLen="28" optLength="692" totalLenIni="697" alignScore="1551.34" chainRmsd="0.91" identity="0.9957" normAlignScore="0.00" probability="8.40e+00" similarity="0.9957" similarity1="97" similarity2="99" totalRmsdIni="1.36" totalRmsdOpt="0.91" ca1Length="715" ca2Length="697" afpNum="4" alignScoreUpdate="0.00" time="-1">`
	`1`	`+<AFPChain name1="1FDO.A" name2="2IV2.X" method="jCE" version="1.1" alnLength="720" blockNum="1" gapLen="28" optLength="692" totalLenIni="697" alignScore="1551.34" chainRmsd="0.91" identity="0.9569" normAlignScore="0.00" probability="8.40e+00" similarity="0.9569" similarity1="97" similarity2="99" totalRmsdIni="1.36" totalRmsdOpt="0.91" ca1Length="715" ca2Length="697" afpNum="4" alignScoreUpdate="0.00" time="-1">`
`2`	`2`	`<block blockNr="0" blockSize="0" blockScore="0.00" blockRmsd="0.91" blockGap="0">`
`3`	`3`	`<eqr eqrNr="0" pdbres1="1" chain1="A" pdbres2="1" chain2="X" />`
`4`	`4`	`<eqr eqrNr="1" pdbres1="2" chain1="A" pdbres2="2" chain2="X" />`