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Commit 7378662

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sblivensbliven
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Add uncommitted changes
1 parent 5f007ec commit 7378662

2 files changed

Lines changed: 11 additions & 10 deletions

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‎biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/AFPChainXMLConverter.java‎

Lines changed: 10 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -244,24 +244,24 @@ public static void printXMLHeader(PrettyXMLWriter xml, AFPChain afpChain) throws
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xml.attribute("optLength", afpChain.getOptLength() + "");
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xml.attribute("totalLenIni", afpChain.getTotalLenIni() + "");
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xml.attribute("alignScore", String.format("%5.2f", afpChain.getAlignScore() ).trim());
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xml.attribute("chainRmsd", String.format("%5.2f", afpChain.getChainRmsd() ).trim());
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xml.attribute("identity",String.format("%5.4f", afpChain.getIdentity() ).trim());
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xml.attribute("normAlignScore", String.format("%5.2f",afpChain.getNormAlignScore()).trim());
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xml.attribute("probability", String.format("%.2e", afpChain.getProbability() ).trim());
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xml.attribute("similarity", String.format("%5.4f", afpChain.getSimilarity() ).trim());
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xml.attribute("alignScore", String.format(Locale.US, "%5.2f", afpChain.getAlignScore() ).trim());
248+
xml.attribute("chainRmsd", String.format(Locale.US, "%5.2f", afpChain.getChainRmsd() ).trim());
249+
xml.attribute("identity",String.format(Locale.US, "%5.4f", afpChain.getIdentity() ).trim());
250+
xml.attribute("normAlignScore", String.format(Locale.US, "%5.2f",afpChain.getNormAlignScore()).trim());
251+
xml.attribute("probability", String.format(Locale.US, "%.2e", afpChain.getProbability() ).trim());
252+
xml.attribute("similarity", String.format(Locale.US, "%5.4f", afpChain.getSimilarity() ).trim());
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xml.attribute("similarity1", afpChain.getCoverage1() + "");
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xml.attribute("similarity2", afpChain.getCoverage2() + "");
256-
xml.attribute("totalRmsdIni", String.format("%5.2f",afpChain.getTotalRmsdIni() ).trim());
257-
xml.attribute("totalRmsdOpt", String.format("%5.2f",afpChain.getTotalRmsdOpt() ).trim());
256+
xml.attribute("totalRmsdIni", String.format(Locale.US, "%5.2f",afpChain.getTotalRmsdIni() ).trim());
257+
xml.attribute("totalRmsdOpt", String.format(Locale.US, "%5.2f",afpChain.getTotalRmsdOpt() ).trim());
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xml.attribute("ca1Length", afpChain.getCa1Length()+"");
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xml.attribute("ca2Length", afpChain.getCa2Length()+"");
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xml.attribute("afpNum",afpChain.getAfpSet().size()+"");
261-
xml.attribute("alignScoreUpdate",String.format("%5.2f",afpChain.getAlignScoreUpdate()).trim());
261+
xml.attribute("alignScoreUpdate",String.format(Locale.US, "%5.2f",afpChain.getAlignScoreUpdate()).trim());
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xml.attribute("time", String.format("%d",afpChain.getCalculationTime()));
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if ( afpChain.getTMScore() != -1){
264-
xml.attribute("tmScore", String.format("%.2f",afpChain.getTMScore()));
264+
xml.attribute("tmScore", String.format(Locale.US, "%.2f",afpChain.getTMScore()));
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}
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// test if alignment is CP:

‎biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/CrystalCell.java‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -24,6 +24,7 @@
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import java.io.Serializable;
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import java.util.ArrayList;
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import java.util.Collections;
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import java.util.Locale;
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//import org.slf4j.Logger;
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//import org.slf4j.LoggerFactory;

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