[Sbfc-svn] SF.net SVN: sbfc:[616] trunk

[<nik...@us...>]

Revision: 616
          http://sourceforge.net/p/sbfc/code/616
Author:   niko-rodrigue
Date:     2016-02-04 16:36:18 +0000 (Thu, 04 Feb 2016)
Log Message:
-----------
using the tidy SBMLWriter for SBMLModel to have better looking resulting xml + updated the version of jsbml used

Modified Paths:
--------------
    trunk/lib/sbfc-1.3.6.jar
    trunk/src/org/sbfc/converter/models/SBMLModel.java

Added Paths:
-----------
    trunk/lib/jsbml-1.2-SNAPSHOT-20160204-with-dependencies.jar
    trunk/lib/jsbml-tidy-1.1.jar
    trunk/lib/jtidy-r938.jar

Removed Paths:
-------------
    trunk/lib/jsbml-1.0-with-dependencies.jar

Deleted: trunk/lib/jsbml-1.0-with-dependencies.jar
===================================================================
(Binary files differ)

Added: trunk/lib/jsbml-1.2-SNAPSHOT-20160204-with-dependencies.jar
===================================================================
(Binary files differ)

Index: trunk/lib/jsbml-1.2-SNAPSHOT-20160204-with-dependencies.jar
===================================================================
--- trunk/lib/jsbml-1.2-SNAPSHOT-20160204-with-dependencies.jar	2016-02-03 13:32:09 UTC (rev 615)
+++ trunk/lib/jsbml-1.2-SNAPSHOT-20160204-with-dependencies.jar	2016-02-04 16:36:18 UTC (rev 616)

Property changes on: trunk/lib/jsbml-1.2-SNAPSHOT-20160204-with-dependencies.jar
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
Added: trunk/lib/jsbml-tidy-1.1.jar
===================================================================
(Binary files differ)

Index: trunk/lib/jsbml-tidy-1.1.jar
===================================================================
--- trunk/lib/jsbml-tidy-1.1.jar	2016-02-03 13:32:09 UTC (rev 615)
+++ trunk/lib/jsbml-tidy-1.1.jar	2016-02-04 16:36:18 UTC (rev 616)

Property changes on: trunk/lib/jsbml-tidy-1.1.jar
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
Added: trunk/lib/jtidy-r938.jar
===================================================================
(Binary files differ)

Index: trunk/lib/jtidy-r938.jar
===================================================================
--- trunk/lib/jtidy-r938.jar	2016-02-03 13:32:09 UTC (rev 615)
+++ trunk/lib/jtidy-r938.jar	2016-02-04 16:36:18 UTC (rev 616)

Property changes on: trunk/lib/jtidy-r938.jar
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
Modified: trunk/lib/sbfc-1.3.6.jar
===================================================================
(Binary files differ)

Modified: trunk/src/org/sbfc/converter/models/SBMLModel.java
===================================================================
--- trunk/src/org/sbfc/converter/models/SBMLModel.java	2016-02-03 13:32:09 UTC (rev 615)
+++ trunk/src/org/sbfc/converter/models/SBMLModel.java	2016-02-04 16:36:18 UTC (rev 616)
@@ -38,6 +38,7 @@
 import org.sbml.jsbml.Model;
 import org.sbml.jsbml.SBMLDocument;
 import org.sbml.jsbml.SBMLException;
+import org.sbml.jsbml.TidySBMLWriter;
 
 
 /**
@@ -98,7 +99,7 @@
 	public void modelToFile(String fileName) throws WriteModelException {
 
 		try {
-			JSBML.writeSBML(document, fileName);
+			new TidySBMLWriter().writeSBMLToFile(document, fileName);
 		} catch (XMLStreamException e) {
 			throw new WriteModelException(e);
 		} catch (IOException e) {
@@ -108,7 +109,6 @@
 		}
 	}
 
-
 	public SBMLDocument modelFromFile(String fileName) throws ReadModelException {
 		
 		try {
@@ -139,7 +139,7 @@
 		String reString =null;
 		
 		try {
-			reString = JSBML.writeSBMLToString(document);
+			reString = new TidySBMLWriter().writeSBMLToString(document);
 		} catch (XMLStreamException e) {
 			throw new WriteModelException(e);
 		} catch (SBMLException e) {

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