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technology mapping tested for covering

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This commit is contained in:
Tramy Nguyen 2019-08-07 23:20:07 -06:00
parent 37f2f422eb
commit dbe40b6d3a
174 changed files with 899659 additions and 31518 deletions
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12
dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/sbol/SBOLFileManager.java
View file

@ -92,7 +92,7 @@ public class SBOLFileManager {
*of which sbol document belong to which sbol file.
*/
fileDocMap.put(sbolFilePath, sbolDoc);
SBOLUtility.getInstance().copyAllTopLevels(sbolDoc, SBOLDOC);
SBOLUtility.getSBOLUtility().copyAllTopLevels(sbolDoc, SBOLDOC);
}
else
sbolFilesAreLoaded = false;
@ -185,11 +185,11 @@ public class SBOLFileManager {
if (sbolFilePath.equals(targetFilePath))
{
for(Sequence s : tempSbolDoc.getSequences())
SBOLUtility.getInstance().addSequence(s, sbolDoc, false);
SBOLUtility.getSBOLUtility().addSequence(s, sbolDoc, false);
for(ComponentDefinition c : tempSbolDoc.getComponentDefinitions())
SBOLUtility.getInstance().addDNAComponent(c, sbolDoc, false);
SBOLUtility.getSBOLUtility().addDNAComponent(c, sbolDoc, false);
}
SBOLUtility.getInstance().writeSBOLDocument(sbolFilePath, sbolDoc);
SBOLUtility.getSBOLUtility().writeSBOLDocument(sbolFilePath, sbolDoc);
//System.out.println("Wrote sbolAnnot to this file: " + sbolFilePath);
}
}
@ -197,8 +197,8 @@ public class SBOLFileManager {
public static void saveDNAComponents(List<ComponentDefinition> dnaComps, String filePath) throws SBOLValidationException, FileNotFoundException, SBOLConversionException {
SBOLDocument sbolDoc = new SBOLDocument();
for (ComponentDefinition dnaComp : dnaComps)
SBOLUtility.getInstance().addDNAComponent(dnaComp, sbolDoc, false);
SBOLUtility.getInstance().writeSBOLDocument(filePath, sbolDoc);
SBOLUtility.getSBOLUtility().addDNAComponent(dnaComp, sbolDoc, false);
SBOLUtility.getSBOLUtility().writeSBOLDocument(filePath, sbolDoc);
}

2
dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/sbol/SBOLUtility.java
View file

@ -57,7 +57,7 @@ public class SBOLUtility
private String sbolURIPrefix;
private static SBOLUtility utility;
public static SBOLUtility getInstance() {
public static SBOLUtility getSBOLUtility() {
if(utility == null) {
utility = new SBOLUtility();
}