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[Jsbml-svn] SF.net SVN: jsbml:[2364] branches/astnode2-merging-alternate
|
From: <nik...@us...> - 2015-10-05 10:00:45
|
Revision: 2364
http://sourceforge.net/p/jsbml/code/2364
Author: niko-rodrigue
Date: 2015-10-05 10:00:41 +0000 (Mon, 05 Oct 2015)
Log Message:
-----------
merged rev 2361
Revision Links:
--------------
http://sourceforge.net/p/jsbml/code/2361
Modified Paths:
--------------
branches/astnode2-merging-alternate/extensions/arrays/src/org/sbml/jsbml/ext/arrays/compiler/VectorCompiler.java
branches/astnode2-merging-alternate/extensions/arrays/src/org/sbml/jsbml/ext/arrays/flattening/ArraysFlattening.java
Property Changed:
----------------
branches/astnode2-merging-alternate/
Index: branches/astnode2-merging-alternate
===================================================================
--- branches/astnode2-merging-alternate 2015-10-05 09:08:27 UTC (rev 2363)
+++ branches/astnode2-merging-alternate 2015-10-05 10:00:41 UTC (rev 2364)
Property changes on: branches/astnode2-merging-alternate
___________________________________________________________________
Modified: svn:mergeinfo
## -1 +1 ##
-/trunk:2191,2194-2195,2197-2200,2202-2206,2209-2213,2216-2220,2222,2224-2244,2246-2248,2251-2262,2280,2293,2296-2297,2301-2305,2307-2310,2313,2318,2320-2321,2325-2326,2332-2333,2343,2348-2352,2354-2359
+/trunk:2191,2194-2195,2197-2200,2202-2206,2209-2213,2216-2220,2222,2224-2244,2246-2248,2251-2262,2280,2293,2296-2297,2301-2305,2307-2310,2313,2318,2320-2321,2325-2326,2332-2333,2343,2348-2352,2354-2359,2361
\ No newline at end of property
Modified: branches/astnode2-merging-alternate/extensions/arrays/src/org/sbml/jsbml/ext/arrays/compiler/VectorCompiler.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/arrays/src/org/sbml/jsbml/ext/arrays/compiler/VectorCompiler.java 2015-10-05 09:08:27 UTC (rev 2363)
+++ branches/astnode2-merging-alternate/extensions/arrays/src/org/sbml/jsbml/ext/arrays/compiler/VectorCompiler.java 2015-10-05 10:00:41 UTC (rev 2364)
@@ -1,4922 +1,4925 @@
-/*
- * $Id$
- * $URL$
- * ----------------------------------------------------------------------------
- * This file is part of JSBML. Please visit <http://sbml.org/Software/JSBML>
- * for the latest version of JSBML and more information about SBML.
- *
- * Copyright (C) 2009-2015 jointly by the following organizations:
- * 1. The University of Tuebingen, Germany
- * 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
- * 3. The California Institute of Technology, Pasadena, CA, USA
- * 4. The University of California, San Diego, La Jolla, CA, USA
- * 5. The Babraham Institute, Cambridge, UK
- * 6. The University of Utah, Salt Lake City, UT, USA
- *
- * This library is free software; you can redistribute it and/or modify it
- * under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation. A copy of the license agreement is provided
- * in the file named "LICENSE.txt" included with this software distribution
- * and also available online as <http://sbml.org/Software/JSBML/License>.
- * ----------------------------------------------------------------------------
- */
-package org.sbml.jsbml.ext.arrays.compiler;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
-
-import org.sbml.jsbml.ASTNode;
-import org.sbml.jsbml.CallableSBase;
-import org.sbml.jsbml.Compartment;
-import org.sbml.jsbml.FunctionDefinition;
-import org.sbml.jsbml.InitialAssignment;
-import org.sbml.jsbml.Model;
-import org.sbml.jsbml.NamedSBase;
-import org.sbml.jsbml.Parameter;
-import org.sbml.jsbml.Quantity;
-import org.sbml.jsbml.SBMLException;
-import org.sbml.jsbml.SBase;
-import org.sbml.jsbml.SpeciesReference;
-import org.sbml.jsbml.ext.arrays.ArraysConstants;
-import org.sbml.jsbml.ext.arrays.ArraysSBasePlugin;
-import org.sbml.jsbml.ext.arrays.Dimension;
-import org.sbml.jsbml.ext.arrays.util.ArraysMath;
-import org.sbml.jsbml.util.Maths;
-import org.sbml.jsbml.util.compilers.ASTNodeCompiler;
-import org.sbml.jsbml.util.compilers.ASTNodeValue;
-
-/**
- * @author Leandro Watanabe
- * @version $Rev$
- * @since 1.0
- * @date Jun 30, 2014
- */
-//TODO: need to check for errors
-//TODO: need to check if its name
-//TODO: SBMLException error id
-//TODO: need to test functions. might have warnings
-public class VectorCompiler implements ASTNodeCompiler {
-
- /**
- *
- */
- private final ASTNodeValue dummy = new ASTNodeValue("dummy", null);
- /**
- *
- */
- private final Model model;
- /**
- *
- */
- private ASTNode node;
- /**
- *
- */
- private Map<String, ASTNode> idToVector;
- /**
- *
- */
- private boolean isSetIdToVector;
- /**
- *
- */
- private final boolean useId;
- /**
- *
- */
- private NamedSBase sbase;
-
- /**
- * @param model
- */
- public VectorCompiler(Model model) {
- this.model = model;
- node = new ASTNode();
- useId = false;
- isSetIdToVector = false;
- }
-
- /**
- * @param model
- * @param useId
- */
- public VectorCompiler(Model model, boolean useId) {
- this.model = model;
- node = new ASTNode();
- this.useId = useId;
- isSetIdToVector = false;
-
- }
-
- /**
- * @param model
- * @param sbase
- * @param useId
- */
- public VectorCompiler(Model model, NamedSBase sbase, boolean useId) {
- this.model = model;
- node = new ASTNode();
- this.useId = useId;
- this.sbase = sbase;
- isSetIdToVector = false;
- }
-
-
-
- /**
- * @param model
- * @param useId
- * @param idToVector
- */
- public VectorCompiler(Model model, boolean useId, Map<String, ASTNode> idToVector) {
- this.model = model;
- node = new ASTNode();
- this.useId = useId;
- this.idToVector = idToVector;
- if (idToVector == null) {
- isSetIdToVector = false;
- } else {
- isSetIdToVector = true;
- }
- }
-
- /**
- * @return
- */
- public ASTNode getNode() {
- return node;
- }
-
- /**
- * @param node
- */
- public void setNode(ASTNode node) {
- this.node = node;
- }
-
- /**
- * @param idToVector
- */
- public void setIdToVector(Map<String, ASTNode> idToVector) {
- this.idToVector = idToVector;
- if (idToVector == null) {
- isSetIdToVector = false;
- } else {
- isSetIdToVector = true;
- }
- }
-
- /**
- *
- */
- public void clearIdToVector() {
- idToVector.clear();
- isSetIdToVector = false;
- }
-
- /**
- * @return
- */
- public boolean isSetIdToVector() {
- if (idToVector != null && isSetIdToVector) {
- return true;
- } else {
- return false;
- }
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.util.compilers.ASTNodeCompiler#abs(org.sbml.jsbml.ASTNode)
- */
- @Override
- public ASTNodeValue abs(ASTNode value) throws SBMLException {
- value.compile(this);
- ASTNode compiled = getNode();
- if (compiled.isVector()) {
- try{
- absRecursive(compiled);
- }
- catch(SBMLException e) {
- unknownValue();
- return dummy;
- }
- }
- else if (useId) {
- if (compiled.toString().equals("unknown")) {
- compiled.setName("unknown");
- } else {
- ASTNode nodeValue = new ASTNode(ASTNode.Type.FUNCTION_ABS, compiled.getParentSBMLObject());
- nodeValue.addChild(compiled);
- setNode(nodeValue);
- }
- return dummy;
- }
- else if (compiled.isNumber()) {
- compiled.setValue(Math.abs(compiled.getReal()));
- }
- else {
- compiled.setName("unknown");
- }
- setNode(compiled);
-
- return dummy;
- }
-
- /**
- * This function calculates the abs value of a vector element-wise.
- *
- * @param value
- * @throws SBMLException
- */
- private void absRecursive(ASTNode value) throws SBMLException{
- for (int i = 0; i < value.getChildCount(); i++) {
- value.getChild(i).compile(this);
- ASTNode child = getNode();
- if (child.isVector()) {
- absRecursive(value.getChild(i));
- } else if (useId){
- ASTNode absValue = new ASTNode(ASTNode.Type.FUNCTION_ABS, child.getParentSBMLObject());
- absValue.addChild(child.clone());
- value.replaceChild(i, absValue);
- } else if (child.isNumber()) {
- value.getChild(i).setValue(Math.abs(child.getReal()));
- } else {
- throw new SBMLException();
- }
- }
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.util.compilers.ASTNodeCompiler#and(java.util.List)
- */
- @Override
- public ASTNodeValue and(List<ASTNode> values) throws SBMLException {
-
- List<ASTNode> vectors = new ArrayList<ASTNode>();
- List<ASTNode> scalars = new ArrayList<ASTNode>();
- List<ASTNode> ids = new ArrayList<ASTNode>();
- boolean success = getScalarsAndVectors(values, vectors, scalars, ids);
-
- if (!success) {
- unknownValue();
- return dummy;
- }
- double sumScalar;
- boolean isSetSumScalar = false;
- boolean hasIds = false;
-
- if (scalars.size() > 0) {
- isSetSumScalar = true;
- }
- if (ids.size() > 0) {
- hasIds = true;
- }
-
- boolean scalarResult = true;
- for (ASTNode node : scalars) {
- scalarResult &= node.getReal() == 1 ? true : false;
- }
- sumScalar = scalarResult ? 1 : 0;
- ASTNode out = new ASTNode(sumScalar);
- if (!vectors.isEmpty()) {
- out = vectors.get(0).clone();
- try {
- andRecursive(vectors, out);
- }
- catch(IndexOutOfBoundsException e) {
- unknownValue();
- return dummy;
- }
- if (isSetSumScalar) {
- scalarVectorAnd(out, new ASTNode(sumScalar));
- }
- if (hasIds) {
- for (ASTNode id : ids) {
- scalarVectorAnd(out, id);
- }
- }
- }
- else {
- if (hasIds) {
- ASTNode result = new ASTNode(ASTNode.Type.LOGICAL_AND, out.getParentSBMLObject());
- if (!ids.isEmpty()) {
- for (int i = 0; i < ids.size(); ++i) {
- result.addChild(ids.get(i).clone());
- }
- }
- out = result;
- }
- if (isSetSumScalar) {
- out.addChild(new ASTNode(sumScalar));
- }
- }
-
- setNode(out);
- return dummy;
- }
-
- /**
- *
- * @param values
- * @param node
- * @throws IndexOutOfBoundsException
- */
- private void andRecursive(List<ASTNode> values, ASTNode node) throws IndexOutOfBoundsException{
- if (!node.isVector()) {
- boolean result = true;
- boolean isResultSet = false;
- node.setType(ASTNode.Type.LOGICAL_AND);
- node.getChildren().clear();
- if (values.size() > 0) {
- for (int i = 0; i < values.size(); ++i) {
- ASTNode value = values.get(i);
- if (value.isNumber()) {
- if (!isResultSet) {
- result = value.getInteger() == 1;
- isResultSet = true;
- } else {
- result &= value.getInteger() == 1 ? true : false;
- }
- } else if (useId) {
- node.addChild(values.get(i).clone());
- } else {
- throw new SBMLException();
- }
- }
- if (isResultSet) {
- node.addChild(new ASTNode(result ? 1 : 0));
- }
- return;
- }
- }
- for (int i = 0; i < node.getChildCount(); ++i) {
- List<ASTNode> nodes = new ArrayList<ASTNode>();
- for (ASTNode value : values) {
- value.compile(this);
- ASTNode result = getNode();
- if (result.isVector()) {
- nodes.add(result.getChild(i));
- }
- }
- andRecursive(nodes, node.getChild(i));
- }
-
- }
-
- /**
- *
- * @param vector
- * @param scalar
- */
- private void scalarVectorAnd(ASTNode vector, ASTNode scalar) {
- for (int i = 0; i < vector.getChildCount(); ++i) {
- ASTNode child = vector.getChild(i);
- child.compile(this);
- ASTNode result = getNode();
- if (result.isVector()) {
- scalarVectorAnd(child, scalar);
- }
- else if (useId) {
- ASTNode nodeValue = new ASTNode(ASTNode.Type.LOGICAL_AND, vector.getChild(i).getParentSBMLObject());
- nodeValue.addChild(result.clone());
- nodeValue.addChild(scalar.clone());
- vector.replaceChild(i, nodeValue);
- }
- else if (result.isNumber()) {
- boolean resBool = result.getReal() == 1 ? true : false;
- boolean scalBool = scalar.getReal() == 1 ? true : false;
- vector.getChild(i).setValue(resBool & scalBool ? 1 : 0);
- }
- else {
- throw new SBMLException();
- }
- }
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.util.compilers.ASTNodeCompiler#arccos(org.sbml.jsbml.ASTNode)
- */
- @Override
- public ASTNodeValue arccos(ASTNode value) throws SBMLException {
- value.compile(this);
- ASTNode compiled = getNode();
- if (compiled.isVector()) {
- try {
- arccosRecursive(compiled);
- }
- catch(SBMLException e) {
- unknownValue();
- return dummy;
- }
- }
- else if (useId) {
- if (compiled.toString().equals("unknown")) {
- compiled.setName("unknown");
- } else {
- ASTNode nodeValue = new ASTNode(ASTNode.Type.FUNCTION_ARCCOS, compiled.getParentSBMLObject());
- nodeValue.addChild(compiled);
- setNode(nodeValue);
- }
- return dummy;
- }
- else if (compiled.isNumber()) {
- compiled.setValue(Math.acos(compiled.getReal()));
- }
- else {
- compiled.setName("unknown");
- }
- setNode(compiled);
-
- return dummy;
- }
-
- /**
- * This function calculates the arcccos value of a vector element-wise.
- *
- * @param value
- * @throws SBMLException
- */
- private void arccosRecursive(ASTNode value) {
- for (int i = 0; i < value.getChildCount(); i++) {
- value.getChild(i).compile(this);
- ASTNode child = getNode();
- if (child.isVector()) {
- arccosRecursive(value.getChild(i));
- } else if (useId){
- ASTNode arccosValue = new ASTNode(ASTNode.Type.FUNCTION_ARCCOS, child.getParentSBMLObject());
- arccosValue.addChild(child.clone());
- value.replaceChild(i, arccosValue);
- } else if (child.isNumber()) {
- value.getChild(i).setValue(Math.acos(child.getReal()));
- } else {
- throw new SBMLException();
- }
- }
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.util.compilers.ASTNodeCompiler#arccosh(org.sbml.jsbml.ASTNode)
- */
- @Override
- public ASTNodeValue arccosh(ASTNode value) throws SBMLException {
- value.compile(this);
- ASTNode compiled = getNode();
- if (compiled.isVector()) {
- try {
- arccoshRecursive(compiled);
- }
- catch(SBMLException e) {
- unknownValue();
- return dummy;
- }
- }
- else if (useId) {
- if (compiled.toString().equals("unknown")) {
- compiled.setName("unknown");
- } else {
- compiled.setName("arccosh(" + compiled.getName() + ")");
- }
- }
- else if (compiled.isNumber()) {
- compiled.setValue(Maths.arccosh(compiled.getReal()));
- }
- else {
- compiled.setName("unknown");
- }
- setNode(compiled);
-
- return dummy;
- }
-
- /**
- * @param value
- * @throws SBMLException
- */
- private void arccoshRecursive(ASTNode value) throws SBMLException {
- for (int i = 0; i < value.getChildCount(); i++) {
- value.getChild(i).compile(this);
- ASTNode child = getNode();
- if (child.isVector()) {
- arccoshRecursive(value.getChild(i));
- } else if (useId){
- ASTNode arccoshValue = new ASTNode(ASTNode.Type.FUNCTION_ARCCOSH, child.getParentSBMLObject());
- arccoshValue.addChild(child.clone());
- value.replaceChild(i, arccoshValue);
- } else if (child.isNumber()) {
- value.getChild(i).setValue(Maths.arccosh(child.getReal()));
- } else {
- throw new SBMLException();
- }
- }
- }
-
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.util.compilers.ASTNodeCompiler#arccot(org.sbml.jsbml.ASTNode)
- */
- @Override
- public ASTNodeValue arccot(ASTNode value) throws SBMLException {
- value.compile(this);
- ASTNode compiled = getNode();
- if (compiled.isVector()) {
- try {
- arccotRecursive(compiled);
- }
- catch(SBMLException e) {
- unknownValue();
- return dummy;
- }
- }
- else if (useId) {
- if (compiled.toString().equals("unknown")) {
- compiled.setName("unknown");
- } else {
- compiled.setName("arccot(" + compiled.getName() + ")");
- }
- }
- else if (compiled.isNumber()) {
- compiled.setValue(Maths.arccot(compiled.getReal()));
- }
- else {
- compiled.setName("unknown");
- }
- setNode(compiled);
-
- return dummy;
- }
-
- /**
- * @param value
- */
- private void arccotRecursive(ASTNode value) {
- for (int i = 0; i < value.getChildCount(); i++) {
- value.getChild(i).compile(this);
- ASTNode child = getNode();
- if (child.isVector()) {
- arccotRecursive(value.getChild(i));
- } else if (useId){
- ASTNode arccotValue = new ASTNode(ASTNode.Type.FUNCTION_ARCCOT, child.getParentSBMLObject());
- arccotValue.addChild(child.clone());
- value.replaceChild(i, arccotValue);
- } else if (child.isNumber()) {
- value.getChild(i).setValue(Maths.arccot(child.getReal()));
- } else {
- throw new SBMLException();
- }
- }
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.util.compilers.ASTNodeCompiler#arccoth(org.sbml.jsbml.ASTNode)
- */
- @Override
- public ASTNodeValue arccoth(ASTNode value) throws SBMLException {
- value.compile(this);
- ASTNode compiled = getNode();
- if (compiled.isVector()) {
- try {
- arccothRecursive(compiled);
- }
- catch(SBMLException e) {
- unknownValue();
- return dummy;
- }
- }
- else if (useId) {
- if (compiled.toString().equals("unknown")) {
- compiled.setName("unknown");
- } else {
- ASTNode nodeValue = new ASTNode(ASTNode.Type.FUNCTION_ARCCOTH, compiled.getParentSBMLObject());
- nodeValue.addChild(compiled);
- setNode(nodeValue);
- }
- return dummy;
- }
- else if (compiled.isNumber()) {
- compiled.setValue(Maths.arccoth(compiled.getReal()));
- }
- else {
- compiled.setName("unknown");
- }
- setNode(compiled);
-
- return dummy;
- }
-
- /**
- * @param value
- */
- private void arccothRecursive(ASTNode value) {
- for (int i = 0; i < value.getChildCount(); i++) {
- value.getChild(i).compile(this);
- ASTNode child = getNode();
- if (child.isVector()) {
- arccothRecursive(value.getChild(i));
- } else if (useId){
- ASTNode arccothValue = new ASTNode(ASTNode.Type.FUNCTION_ARCCOTH, child.getParentSBMLObject());
- arccothValue.addChild(child.clone());
- value.replaceChild(i, arccothValue);
- } else if (child.isNumber()) {
- value.getChild(i).setValue(Maths.arccoth(child.getReal()));
- } else {
- throw new SBMLException();
- }
- }
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.util.compilers.ASTNodeCompiler#arccsc(org.sbml.jsbml.ASTNode)
- */
- @Override
- public ASTNodeValue arccsc(ASTNode value) throws SBMLException {
- value.compile(this);
- ASTNode compiled = getNode();
- if (compiled.isVector()) {
- try {
- arccscRecursive(compiled);
- }
- catch(SBMLException e) {
- unknownValue();
- return dummy;
- }
- }
- else if (useId) {
- if (compiled.toString().equals("unknown")) {
- compiled.setName("unknown");
- } else {
- ASTNode nodeValue = new ASTNode(ASTNode.Type.FUNCTION_ARCCSC, compiled.getParentSBMLObject());
- nodeValue.addChild(compiled);
- setNode(nodeValue);
- }
- return dummy;
- }
- else if (compiled.isNumber()) {
- compiled.setValue(Maths.arccsc(compiled.getReal()));
- }
- else {
- compiled.setName("unknown");
- }
- setNode(compiled);
-
- return dummy;
- }
-
- /**
- * @param value
- */
- private void arccscRecursive(ASTNode value) {
- for (int i = 0; i < value.getChildCount(); i++) {
- value.getChild(i).compile(this);
- ASTNode child = getNode();
- if (child.isVector()) {
- arccscRecursive(value.getChild(i));
- } else if (useId){
- ASTNode arccscValue = new ASTNode(ASTNode.Type.FUNCTION_ARCCSC, child.getParentSBMLObject());
- arccscValue.addChild(child.clone());
- value.replaceChild(i, arccscValue);
- } else if (child.isNumber()) {
- value.getChild(i).setValue(Maths.arccsc(child.getReal()));
- } else {
- throw new SBMLException();
- }
- }
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.util.compilers.ASTNodeCompiler#arccsch(org.sbml.jsbml.ASTNode)
- */
- @Override
- public ASTNodeValue arccsch(ASTNode value) throws SBMLException {
- value.compile(this);
- ASTNode compiled = getNode();
- if (compiled.isVector()) {
- try {
- arccschRecursive(compiled);
- }
- catch(SBMLException e) {
- unknownValue();
- return dummy;
- }
- }
- else if (useId) {
- if (compiled.toString().equals("unknown")) {
- compiled.setName("unknown");
- } else {
- ASTNode nodeValue = new ASTNode(ASTNode.Type.FUNCTION_ARCCSCH, compiled.getParentSBMLObject());
- nodeValue.addChild(compiled);
- setNode(nodeValue);
- }
- return dummy;
- }
- else if (compiled.isNumber()) {
- compiled.setValue(Maths.arccsch(compiled.getReal()));
- }
- else {
- compiled.setName("unknown");
- }
- setNode(compiled);
-
- return dummy;
- }
-
- /**
- * @param value
- */
- private void arccschRecursive(ASTNode value) {
- for (int i = 0; i < value.getChildCount(); i++) {
- value.getChild(i).compile(this);
- ASTNode child = getNode();
- if (child.isVector()) {
- arccschRecursive(value.getChild(i));
- } else if (useId){
- ASTNode arccschValue = new ASTNode(ASTNode.Type.FUNCTION_ARCCSCH, child.getParentSBMLObject());
- arccschValue.addChild(child.clone());
- value.replaceChild(i, arccschValue);
- } else if (child.isNumber()) {
- value.getChild(i).setValue(Maths.arccsch(child.getReal()));
- } else{
- throw new SBMLException();
- }
- }
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.util.compilers.ASTNodeCompiler#arcsec(org.sbml.jsbml.ASTNode)
- */
- @Override
- public ASTNodeValue arcsec(ASTNode value) throws SBMLException {
- value.compile(this);
- ASTNode compiled = getNode();
- if (compiled.isVector()) {
- try {
- arcsecRecursive(compiled);
- }
- catch(SBMLException e) {
- unknownValue();
- return dummy;
- }
- } else if (useId) {
- if (compiled.toString().equals("unknown")) {
- compiled.setName("unknown");
- } else {
- ASTNode nodeValue = new ASTNode(ASTNode.Type.FUNCTION_ARCSEC, compiled.getParentSBMLObject());
- nodeValue.addChild(compiled);
- setNode(nodeValue);
- }
- return dummy;
- } else if (compiled.isNumber()) {
- compiled.setValue(Maths.arcsec(compiled.getReal()));
- } else {
- compiled.setName("unknown");
- }
- setNode(compiled);
-
- return dummy;
- }
-
- /**
- * @param value
- */
- private void arcsecRecursive(ASTNode value) {
- for (int i = 0; i < value.getChildCount(); i++) {
- value.getChild(i).compile(this);
- ASTNode child = getNode();
- if (child.isVector()) {
- arcsecRecursive(value.getChild(i));
- } else if (useId){
- ASTNode arcsecValue = new ASTNode(ASTNode.Type.FUNCTION_ARCSEC, child.getParentSBMLObject());
- arcsecValue.addChild(child.clone());
- value.replaceChild(i, arcsecValue);
- } else if (child.isNumber()) {
- value.getChild(i).setValue(Maths.arcsec(child.getReal()));
- } else {
- throw new SBMLException();
- }
- }
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.util.compilers.ASTNodeCompiler#arcsech(org.sbml.jsbml.ASTNode)
- */
- @Override
- public ASTNodeValue arcsech(ASTNode value) throws SBMLException {
- value.compile(this);
- ASTNode compiled = getNode();
- if (compiled.isVector()) {
- try {
- arcsechRecursive(compiled);
- }
- catch(SBMLException e) {
- unknownValue();
- return dummy;
- }
- }
- else if (useId) {
- if (compiled.toString().equals("unknown")) {
- compiled.setName("unknown");
- } else {
- ASTNode nodeValue = new ASTNode(ASTNode.Type.FUNCTION_ARCSECH, compiled.getParentSBMLObject());
- nodeValue.addChild(compiled);
- setNode(nodeValue);
- }
- return dummy;
- }
- else if (compiled.isNumber()) {
- compiled.setValue(Maths.arcsech(compiled.getReal()));
- }
-
- else {
- compiled.setName("unknown");
- }
- setNode(compiled);
-
- return dummy;
- }
-
- /**
- * @param value
- */
- private void arcsechRecursive(ASTNode value) {
- for (int i = 0; i < value.getChildCount(); i++) {
- value.getChild(i).compile(this);
- ASTNode child = getNode();
- if (child.isVector()) {
- arcsechRecursive(value.getChild(i));
- } else if (useId){
- ASTNode arcsechValue = new ASTNode(ASTNode.Type.FUNCTION_ARCSECH, child.getParentSBMLObject());
- arcsechValue.addChild(child.clone());
- value.replaceChild(i, arcsechValue);
- } else if (child.isNumber()) {
- value.getChild(i).setValue(Maths.arcsech(child.getReal()));
- } else {
- throw new SBMLException();
- }
- }
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.util.compilers.ASTNodeCompiler#arcsin(org.sbml.jsbml.ASTNode)
- */
- @Override
- public ASTNodeValue arcsin(ASTNode value) throws SBMLException {
- value.compile(this);
- ASTNode compiled = getNode();
- if (compiled.isVector()) {
- try {
- arcsinRecursive(compiled);
- }
- catch(SBMLException e) {
- unknownValue();
- return dummy;
- }
- }
- else if (useId) {
- if (compiled.toString().equals("unknown")) {
- compiled.setName("unknown");
- } else {
- ASTNode nodeValue = new ASTNode(ASTNode.Type.FUNCTION_ARCSIN, compiled.getParentSBMLObject());
- nodeValue.addChild(compiled);
- setNode(nodeValue);
- }
- return dummy;
- }
- else if (compiled.isNumber()) {
- compiled.setValue(Math.asin(compiled.getReal()));
- }
-
- else {
- compiled.setName("unknown");
- }
- setNode(compiled);
-
- return dummy;
- }
-
- /**
- * @param value
- */
- private void arcsinRecursive(ASTNode value) {
- for (int i = 0; i < value.getChildCount(); i++) {
- value.getChild(i).compile(this);
- ASTNode child = getNode();
- if (child.isVector()) {
- arcsinRecursive(value.getChild(i));
- } else if (useId){
- ASTNode arcsinValue = new ASTNode(ASTNode.Type.FUNCTION_ARCSIN, child.getParentSBMLObject());
- arcsinValue.addChild(child.clone());
- value.replaceChild(i, arcsinValue);
- } else if (child.isNumber()) {
- value.getChild(i).setValue(Math.asin(child.getReal()));
- } else {
- throw new SBMLException();
- }
- }
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.util.compilers.ASTNodeCompiler#arcsinh(org.sbml.jsbml.ASTNode)
- */
- @Override
- public ASTNodeValue arcsinh(ASTNode value) throws SBMLException {
- value.compile(this);
- ASTNode compiled = getNode();
- if (compiled.isVector()) {
- arcsinhRecursive(compiled);
- }
- else if (useId) {
- if (compiled.toString().equals("unknown")) {
- compiled.setName("unknown");
- } else {
- ASTNode nodeValue = new ASTNode(ASTNode.Type.FUNCTION_ARCSINH, compiled.getParentSBMLObject());
- nodeValue.addChild(compiled);
- setNode(nodeValue);
- }
- return dummy;
- }
- else if (compiled.isNumber()) {
- compiled.setValue(Maths.arcsinh(compiled.getReal()));
- }
- else {
- compiled.setName("unknown");
- }
- setNode(compiled);
-
- return dummy;
- }
-
- /**
- * @param value
- */
- private void arcsinhRecursive(ASTNode value) {
- for (int i = 0; i < value.getChildCount(); i++) {
- value.getChild(i).compile(this);
- ASTNode child = getNode();
- if (child.isVector()) {
- arcsinhRecursive(value.getChild(i));
- } else if (useId){
- ASTNode arcsinhValue = new ASTNode(ASTNode.Type.FUNCTION_ARCSINH, child.getParentSBMLObject());
- arcsinhValue.addChild(child.clone());
- value.replaceChild(i, arcsinhValue);
- } else if (child.isNumber()) {
- value.getChild(i).setValue(Maths.arcsinh(child.getReal()));
- } else {
- throw new SBMLException();
- }
- }
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.util.compilers.ASTNodeCompiler#arctan(org.sbml.jsbml.ASTNode)
- */
- @Override
- public ASTNodeValue arctan(ASTNode value) throws SBMLException {
- value.compile(this);
- ASTNode compiled = getNode();
- if (compiled.isVector()) {
- try {
- arctanRecursive(compiled);
- }
- catch(SBMLException e) {
- unknownValue();
- return dummy;
- }
- }
- else if (useId) {
- if (compiled.toString().equals("unknown")) {
- compiled.setName("unknown");
- } else {
- ASTNode nodeValue = new ASTNode(ASTNode.Type.FUNCTION_ARCTAN, compiled.getParentSBMLObject());
- nodeValue.addChild(compiled);
- setNode(nodeValue);
- }
- return dummy;
- }
- else if (compiled.isNumber()) {
- compiled.setValue(Math.atan(compiled.getReal()));
- }
- else {
- compiled.setName("unknown");
- }
- setNode(compiled);
-
- return dummy;
- }
-
- /**
- * @param value
- */
- private void arctanRecursive(ASTNode value) {
- for (int i = 0; i < value.getChildCount(); i++) {
- value.getChild(i).compile(this);
- ASTNode child = getNode();
- if (child.isVector()) {
- arctanRecursive(value.getChild(i));
- } else if (useId){
- ASTNode arctanValue = new ASTNode(ASTNode.Type.FUNCTION_ARCTAN, child.getParentSBMLObject());
- arctanValue.addChild(child.clone());
- value.replaceChild(i, arctanValue);
- } else if (child.isNumber()) {
- value.getChild(i).setValue(Math.atan(child.getReal()));
- } else {
- throw new SBMLException();
- }
- }
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.util.compilers.ASTNodeCompiler#arctanh(org.sbml.jsbml.ASTNode)
- */
- @Override
- public ASTNodeValue arctanh(ASTNode value) throws SBMLException {
- value.compile(this);
- ASTNode compiled = getNode();
- if (compiled.isVector()) {
- try {
- arctanhRecursive(compiled);
- }
- catch(SBMLException e) {
- unknownValue();
- return dummy;
- }
- }
- else if (useId) {
- if (compiled.toString().equals("unknown")) {
- compiled.setName("unknown");
- } else {
- ASTNode nodeValue = new ASTNode(ASTNode.Type.FUNCTION_ARCTANH, compiled.getParentSBMLObject());
- nodeValue.addChild(compiled);
- setNode(nodeValue);
- }
- return dummy;
- }
- else if (compiled.isNumber()) {
- compiled.setValue(Maths.arctanh(compiled.getReal()));
- }
- else {
- compiled.setName("unknown");
- }
- setNode(compiled);
-
- return dummy;
- }
-
- /**
- * @param value
- */
- private void arctanhRecursive(ASTNode value) {
- for (int i = 0; i < value.getChildCount(); i++) {
- value.getChild(i).compile(this);
- ASTNode child = getNode();
- if (child.isVector()) {
- arctanhRecursive(value.getChild(i));
- } else if (useId){
- ASTNode arctanhValue = new ASTNode(ASTNode.Type.FUNCTION_ARCTANH, child.getParentSBMLObject());
- arctanhValue.addChild(child.clone());
- value.replaceChild(i, arctanhValue);
- } else if (child.isNumber()) {
- value.getChild(i).setValue(Maths.arctanh(child.getReal()));
- } else {
- throw new SBMLException();
- }
- }
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.util.compilers.ASTNodeCompiler#ceiling(org.sbml.jsbml.ASTNode)
- */
- @Override
- public ASTNodeValue ceiling(ASTNode value) throws SBMLException {
- value.compile(this);
- ASTNode compiled = getNode();
- if (compiled.isVector()) {
- try {
- ceilingRecursive(compiled);
- }
- catch(SBMLException e) {
- unknownValue();
- return dummy;
- }
- }
- else if (useId) {
- if (compiled.toString().equals("unknown")) {
- compiled.setName("unknown");
- } else {
- ASTNode nodeValue = new ASTNode(ASTNode.Type.FUNCTION_CEILING, compiled.getParentSBMLObject());
- nodeValue.addChild(compiled);
- setNode(nodeValue);
- }
- return dummy;
- }
- else if (compiled.isNumber()) {
- compiled.setValue(Math.ceil(compiled.getReal()));
- }
- else {
- compiled.setName("unknown");
- }
- setNode(compiled);
-
- return dummy;
- }
-
- /**
- * @param value
- */
- private void ceilingRecursive(ASTNode value) {
- for (int i = 0; i < value.getChildCount(); i++) {
- value.getChild(i).compile(this);
- ASTNode child = getNode();
- if (child.isVector()) {
- ceilingRecursive(value.getChild(i));
- } else if (useId){
- ASTNode ceilValue = new ASTNode(ASTNode.Type.FUNCTION_CEILING, child.getParentSBMLObject());
- ceilValue.addChild(child.clone());
- value.replaceChild(i, ceilValue);
- } else if (child.isNumber()) {
- value.getChild(i).setValue(Math.ceil(child.getReal()));
- } else {
- throw new SBMLException();
- }
- }
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.util.compilers.ASTNodeCompiler#compile(org.sbml.jsbml.Compartment)
- */
- @Override
- public ASTNodeValue compile(Compartment c) {
- if (useId) {
- transformNamedSBase(c);
- } else {
- transformSBase(c);
- }
- return dummy;
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.util.compilers.ASTNodeCompiler#compile(double, int, java.lang.String)
- */
- @Override
- public ASTNodeValue compile(double mantissa, int exponent, String units) {
- ASTNode node = new ASTNode();
- node.setValue(mantissa, exponent);
- setNode(node);
- return dummy;
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.util.compilers.ASTNodeCompiler#compile(double, java.lang.String)
- */
- @Override
- public ASTNodeValue compile(double real, String units) {
- setNode(new ASTNode(real));
- return dummy;
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.util.compilers.ASTNodeCompiler#compile(int, java.lang.String)
- */
- @Override
- public ASTNodeValue compile(int integer, String units) {
- setNode(new ASTNode(integer));
- return dummy;
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.util.compilers.ASTNodeCompiler#compile(org.sbml.jsbml.CallableSBase)
- */
- @Override
- public ASTNodeValue compile(CallableSBase variable) throws SBMLException {
- if (useId) {
- transformNamedSBase(variable);
- }
- else {
- transformSBase(variable);
- }
- return dummy;
- }
-
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.util.compilers.ASTNodeCompiler#compile(java.lang.String)
- */
- @Override
- public ASTNodeValue compile(String name) {
-
- if(isSetIdToVector() && idToVector.containsKey(name))
- {
- setNode(idToVector.get(name));
- }
- else
- {
- SBase sbase = model.findNamedSBase(name);
- if (sbase != null) {
- if (useId) {
- if (isSetIdToVector() && idToVector.containsKey(name)) {
- setNode(idToVector.get(name));
- } else {
- transformNamedSBase(sbase);
- }
- } else {
- transformSBase(sbase);
- }
- }
- else if (this.sbase != null && this.sbase.getId().equals(name)) {
- if (useId) {
- if (isSetIdToVector() && idToVector.containsKey(name)) {
- setNode(idToVector.get(name));
- } else {
- transformNamedSBase(this.sbase);
- }
- } else {
- transformSBase(this.sbase);
- }
- }
- else
- {
- if (useId) {
- setNode(new ASTNode(name));
- }
- else {
- unknownValue();
- }
- }
- }
- return dummy;
- }
-
- /**
- * @param sbase
- */
- private void transformNamedSBase(SBase sbase) {
- ArraysSBasePlugin arraysPlugin = (ArraysSBasePlugin) sbase.getExtension(ArraysConstants.shortLabel);
- if (arraysPlugin == null || arraysPlugin.getDimensionCount() == 0) {
- if (sbase instanceof FunctionDefinition) {
- FunctionDefinition namedSBase = (FunctionDefinition) sbase;
- ASTNode func = new ASTNode(ASTNode.Type.FUNCTION);
- func.setName(namedSBase.getId());
- setNode(func);
- }
- else if (sbase instanceof NamedSBase) {
- NamedSBase namedSBase = (NamedSBase) sbase;
- setNode(new ASTNode(namedSBase.getId()));
- }
- else {
- unknownValue();
- }
- }
- else {
- if (sbase instanceof SpeciesReference) {
- SpeciesReference ref = (SpeciesReference) sbase;
- setNode(constructVector(arraysPlugin, ref));
-
- }
- else if (sbase instanceof NamedSBase) {
- NamedSBase namedSBase = (NamedSBase) sbase;
- setNode(constructVector(arraysPlugin, namedSBase));
- }
- else {
- unknownValue();
- }
- }
- }
-
- /**
- * @param arraysPlugin
- * @param sbase
- * @return
- */
- private ASTNode constructVector(ArraysSBasePlugin arraysPlugin, NamedSBase sbase) {
- String id = sbase.getId();
- Dimension dim = arraysPlugin.getDimensionByArrayDimension(0);
- double size = ArraysMath.getSize(model, dim);
- List<ASTNode> vector = new ArrayList<ASTNode>((int) size);
- for (int i = 0; i < size; ++i) {
- vector.add(new ASTNode("_" + i));
- }
- vector(vector);
- ASTNode vectorNode = getNode();
- for (int i = 1; i < arraysPlugin.getDimensionCount(); ++i) {
- dim = arraysPlugin.getDimensionByArrayDimension(i);
- size = ArraysMath.getSize(model, dim);
- vector = new ArrayList<ASTNode>((int) size);
- for (int j = 0; j < size; ++j) {
- ASTNode clone = vectorNode.clone();
- updateASTNodeName(clone, j);
- //TODO check if clone is unique
- vector.add(clone);
- }
- vector(vector);
- vectorNode = getNode();
- }
- updateASTNodeName(vectorNode, id);
- return vectorNode;
- }
-
- /**
- * @param arraysPlugin
- * @param quantity
- * @return
- */
- private ASTNode constructVector(ArraysSBasePlugin arraysPlugin, Quantity quantity) {
- double value = quantity.getValue();
- Dimension dim = arraysPlugin.getDimensionByArrayDimension(0);
- Parameter p = model.getParameter(dim.getSize());
- double size = p.getValue();
- List<ASTNode> vector = new ArrayList<ASTNode>((int) size);
- for (int j = 0; j < size; ++j) {
- vector.add(new ASTNode(value));
- }
- vector(vector);
- ASTNode vectorNode = getNode();
- for (int i = 1; i < arraysPlugin.getDimensionCount(); ++i) {
- dim = arraysPlugin.getDimensionByArrayDimension(i);
- p = model.getParameter(dim.getSize());
- size = p.getValue();
- vector = new ArrayList<ASTNode>((int) size);
- for (int j = 0; j < size; ++j) {
- vector.add(vectorNode);
- }
- vector(vector);
- vectorNode = getNode();
- }
-
- return vectorNode;
- }
-
- /**
- * @param arraysPlugin
- * @param node
- * @return
- */
- private ASTNode constructVector(ArraysSBasePlugin arraysPlugin, ASTNode node) {
-
- Dimension dim = arraysPlugin.getDimensionByArrayDimension(0);
- Parameter p = model.getParameter(dim.getSize());
- double size = p.getValue();
- List<ASTNode> vector = new ArrayList<ASTNode>((int) size);
- for (int j = 0; j < size; ++j) {
- vector.add(node.clone());
- }
- vector(vector);
- ASTNode vectorNode = getNode();
- for (int i = 1; i < arraysPlugin.getDimensionCount(); ++i) {
- dim = arraysPlugin.getDimensionByArrayDimension(i);
- p = model.getParameter(dim.getSize());
- size = p.getValue();
- vector = new ArrayList<ASTNode>((int) size);
- for (int j = 0; j < size; ++j) {
- vector.add(vectorNode);
- }
- vector(vector);
- vectorNode = getNode();
- }
-
- return vectorNode;
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.util.compilers.ASTNodeCompiler#cos(org.sbml.jsbml.ASTNode)
- */
- @Override
- public ASTNodeValue cos(ASTNode value) throws SBMLException {
- value.compile(this);
- ASTNode compiled = getNode();
- if (compiled.isVector()) {
- try{
- cosRecursive(compiled);
- }
- catch(SBMLException e) {
- unknownValue();
- return dummy;
- }
- }
- else if (useId) {
- if (compiled.toString().equals("unknown")) {
- compiled.setName("unknown");
- } else {
- ASTNode nodeValue = new ASTNode(ASTNode.Type.FUNCTION_COS, compiled.getParentSBMLObject());
- nodeValue.addChild(compiled);
- setNode(nodeValue);
- }
- return dummy;
- }
- else if (compiled.isNumber()) {
- compiled.setValue(Math.cos(compiled.getReal()));
- }
-
- else {
- compiled.setName("unknown");
- }
- setNode(compiled);
-
- return dummy;
- }
-
- /**
- * @param value
- */
- private void cosRecursive(ASTNode value) {
- for (int i = 0; i < value.getChildCount(); i++) {
- value.getChild(i).compile(this);
- ASTNode child = getNode();
- if (child.isNumber()) {
- value.getChild(i).setValue(Math.cos(child.getReal()));
- } else if (child.isVector()) {
- cosRecursive(value.getChild(i));
- } else if (useId){
- ASTNode cosValue = new ASTNode(ASTNode.Type.FUNCTION_COS, child.getParentSBMLObject());
- cosValue.addChild(child.clone());
- value.replaceChild(i, cosValue);
- } else {
- throw new SBMLException();
- }
- }
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.util.compilers.ASTNodeCompiler#cosh(org.sbml.jsbml.ASTNode)
- */
- @Override
- public ASTNodeValue cosh(ASTNode value) throws SBMLException {
- value.compile(this);
- ASTNode compiled = getNode();
- if (compiled.isVector()) {
- try {
- coshRecursive(compiled);
- }
- catch(SBMLException e) {
- unknownValue();
- return dummy;
- }
- }
- else if (useId) {
- if (compiled.toString().equals("unknown")) {
- compiled.setName("unknown");
- } else {
- ASTNode nodeValue = new ASTNode(ASTNode.Type.FUNCTION_COSH, compiled.getParentSBMLObject());
- nodeValue.addChild(compiled);
- setNode(nodeValue);
- }
- return dummy;
- }
- else if (compiled.isNumber()) {
- compiled.setValue(Math.cosh(compiled.getReal()));
- }
- else {
- compiled.setName("unknown");
- }
- setNode(compiled);
-
- return dummy;
- }
-
- /**
- * @param value
- */
- private void coshRecursive(ASTNode value) {
- for (int i = 0; i < value.getChildCount(); i++) {
- value.getChild(i).compile(this);
- ASTNode child = getNode();
- if (child.isNumber()) {
- value.getChild(i).setValue(Math.cosh(child.getReal()));
- } else if (child.isVector()) {
- coshRecursive(value.getChild(i));
- } else if (useId){
- ASTNode coshValue = new ASTNode(ASTNode.Type.FUNCTION_COSH, child.getParentSBMLObject());
- coshValue.addChild(child.clone());
- value.replaceChild(i, coshValue);
- } else {
- throw new SBMLException();
- }
- }
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.util.compilers.ASTNodeCompiler#cot(org.sbml.jsbml.ASTNode)
- */
- @Override
- public ASTNodeValue cot(ASTNode value) throws SBMLException {
- value.compile(this);
- ASTNode compiled = getNode();
- if (compiled.isVector()) {
- try {
- cotRecursive(compiled);
- }
- catch(SBMLException e) {
- unknownValue();
- return dummy;
- }
- }
- else if (useId) {
- if (compiled.toString().equals("unknown")) {
- compiled.setName("unknown");
- } else {
- ASTNode nodeValue = new ASTNode(ASTNode.Type.FUNCTION_COT, compiled.getParentSBMLObject());
- nodeValue.addChild(compiled);
- setNode(nodeValue);
- }
- return dummy;
- }
- else if (compiled.isNumber()) {
- compiled.setValue(Maths.cot(compiled.getReal()));
- }
- else {
- compiled.setName("unknown");
- }
- setNode(compiled);
-
- return dummy;
- }
-
- /**
- * @param value
- */
- private void cotRecursive(ASTNode value) {
- for (int i = 0; i < value.getChildCount(); i++) {
- value.getChild(i).compile(this);
- ASTNode child = getNode();
- if (child.isNumber()) {
- value.getChild(i).setValue(Maths.cot(child.getReal()));
- } else if (child.isVector()) {
- cotRecursive(value.getChild(i));
- } else if (useId){
- ASTNode cotValue = new ASTNode(ASTNode.Type.FUNCTION_COT, child.getParentSBMLObject());
- cotValue.addChild(child.clone());
- value.replaceChild(i, cotValue);
- } else {
- throw new SBMLException();
- }
- }
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.util.compilers.ASTNodeCompiler#coth(org.sbml.jsbml.ASTNode)
- */
- @Override
- public ASTNodeValue coth(ASTNode value) throws SBMLException {
- value.compile(this);
- ASTNode compiled = getNode();
- if (compiled.isVector()) {
- try {
- cothRecursive(compiled);
- }
- catch(SBMLException e) {
- unknownValue();
- return dummy;
- }
- }
- else if (useId) {
- if (compiled.toString().equals("unknown")) {
- compiled.setName("unknown");
- } else {
- ASTNode nodeValue = new ASTNode(ASTNode.Type.FUNCTION_COTH, compiled.getParentSBMLObject());
- nodeValue.addChild(compiled);
- setNode(nodeValue);
- }
- return dummy;
- }
- else if (compiled.isNumber()) {
- compiled.setValue(Maths.coth(compiled.getReal()));
- }
- else {
- compiled.setName("unknown");
- }
- setNode(compiled);
-
- return dummy;
- }
-
- /**
- * @param value
- */
- private void cothRecursive(ASTNode value) {
- for (int i = 0; i < value.getChildCount(); i++) {
- value.getChild(i).compile(this);
- ASTNode child = getNode();
- if (child.isVector()) {
- cothRecursive(value.getChild(i));
- } else if (useId){
- ASTNode cothValue = new ASTNode(ASTNode.Type.FUNCTION_COTH, child.getParentSBMLObject());
- cothValue.addChild(child.clone());
- value.replaceChild(i, cothValue);
- } else if (child.isNumber()) {
- value.getChild(i).setValue(Maths.coth(child.getReal()));
- } else {
- throw new SBMLException();
- }
- }
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.util.compilers.ASTNodeCompiler#csc(org.sbml.jsbml.ASTNode)
- */
- @Override
- public ASTNodeValue csc(ASTNode value) throws SBMLException {
- value.compile(this);
- ASTNode compiled = getNode();
- if (compiled.isVector()) {
- try {
- cscRecursive(compiled);
- }
- catch(SBMLException e) {
- unknownValue();
- return dummy;
- }
- }
- else if (useId) {
- if (compiled.toString().equals("unknown")) {
- compiled.setName("unknown");
- } else {
- ASTNode nodeValue = new ASTNode(ASTNode.Type.FUNCTION_CSC, compiled.getParentSBMLObject());
- nodeValue.addChild(compiled);
- setNode(nodeValue);
- }
- return dummy;
- }
- else if (compiled.isNumber()) {
- compiled.setValue(Maths.csc(compiled.getReal()));
- }
- else {
- compiled.setName("unknown");
- }
- setNode(compiled);
-
- return dummy;
- }
-
- /**
- * @param value
- */
- private void cscRecursive(ASTNode value) {
- for (int i = 0; i < value.getChildCount(); i++) {
- value.getChild(i).compile(this);
- ASTNode child = getNode();
- if (child.isVector()) {
- cscRecursive(value.getChild(i));
- } else if (useId){
- ASTNode cscValue = new ASTNode(ASTNode.Type.FUNCTION_CSC, child.getParentSBMLObject());
- cscValue.addChild(child.clone());
- value.replaceChild(i, cscValue);
- } else if (child.isNumber()) {
- value.getChild(i).setValue(Maths.csc(child.getReal()));
- } else {
- throw new SBMLException();
- }
- }
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.util.compilers.ASTNodeCompiler#csch(org.sbml.jsbml.ASTNode)
- */
- @Override
- public ASTNodeValue csch(ASTNode value) throws SBMLException {
- value.compile(this);
- ASTNode compiled = getNode();
- if (compiled.isVector()) {
- try {
- cschRecursive(compiled);
- }
- catch(SBMLException e) {
- unknownValue();
- return dummy;
- }
- }
- else if (useId) {
- if (compiled.toString().equals("unknown")) {
- compiled.setName("unknown");
- } else {
- ASTNode nodeValue = new ASTNode(ASTNode.Type.FUNCTION_CSCH, compiled.getParentSBMLObject());
- nodeValue.addChild(compiled);
- setNode(nodeValue);
- }
- return dummy;
- }
- else if (compiled.isNumber()) {
- compiled.setValue(Maths.csch(compiled.getReal()));
- }
-
- else {
- compiled.setName("unknown");
- }
- setNode(compiled);
-
- return dummy;
- }
-
- /**
- * @param value
- */
- private void cschRecursive(ASTNode value) {
- for (int i = 0; i < value.getChildCount(); i++) {
- value.getChild(i).compile(this);
- ASTNode child = getNode();
- if (child.isVector()) {
- cschRecursive(value.getChild(i));
- } else if (useId){
- ASTNode cschValue = new ASTNode(ASTNode.Type.FUNCTION_CSCH, child.getParentSBMLObject());
- cschValue.addChild(child.clone());
- value.replaceChild(i, cschValue);
- } else if (child.isNumber()) {
- value.getChild(i).setValue(Maths.csch(child.getReal()));
- } else {
- throw new SBMLException();
- }
- }
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.util.compilers.ASTNodeCompiler#delay(java.lang.String, org.sbml.jsbml.ASTNode, org.sbml.jsbml.ASTNode, java.lang.String)
- */
- @Override
- public ASTNodeValue delay(String delayName, ASTNode x, ASTNode delay,
- String timeUnits) throws SBMLException {
- // TODO Auto-generated method stub
- unknownValue();
- return dummy;
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.util.compilers.ASTNodeCompiler#eq(org.sbml.jsbml.ASTNode, org.sbml.jsbml.ASTNode)
- */
- @Override
- public ASTNodeValue eq(ASTNode left, ASTNode right) throws SBMLException {
- left.compile(this);
- ASTNode leftCompiled = getNode();
- right.compile(this);
- ASTNode rightCompiled = getNode();
-
- if (leftCompiled.isVector()) {
- if (rightCompiled.isVector()) {
- ASTNode result = leftCompiled.clone();
- try {
- eqRecursive(rightCompiled,leftCompiled, result);
- }
- catch(SBMLException e) {
- unknownValue();
- return dummy;
- }
- setNode(result);
-
- } else if (rightCompiled.isNumber() || useId) {
- ASTNode result = leftCompiled.clone();
- try {
- scalarVectorEq(result, rightCompiled);
- }
- catch(SBMLException e) {
- unknownValue();
- return dummy;
- }
- setNode(result);
-
- } else {
- unknownValue();
- }
- }
- else if (leftCompiled.isNumber() || useId) {
- if (rightCompiled.isVector()) {
- ASTNode result = rightCompiled.clone();
- try {
- scalarVectorEq(result, leftCompiled);
- }
- catch(SBMLException e) {
- unknownValue();
- return dummy;
- }
- setNode(result);
- } else if (useId) {
- if (leftCompiled.toString().equals("unknown") || rightCompiled.toString().equals("unknown")) {
- unknownValue();
- } else {
- ASTNode result = new ASTNode(ASTNode.Type.RELATIONAL_EQ);
- result.addChild(leftCompiled);
- result.addChild(rightCompiled);
- setNode(result);
- }
- } else if (leftCompiled.isNumber() && rightCompiled.isNumber()) {
- double leftValue = leftCompiled.getReal();
- double rightValue = rightCompiled.getReal();
- ASTNode result = new ASTNode(leftValue == rightValue ? 1 : 0, left.getParentSBMLObject());
- setNode(result);
- } else {
- unknownValue();
- }
- } else {
- unknownValue();
- }
- return dummy;
- }
-
- /**
- *
- * @param right
- * @param left
- * @param node
- * @throws IndexOutOfBoundsException
- * @throws SBMLException
- */
- private void eqRecursive(ASTNode right, ASTNode left, ASTNode node) throws IndexOutOfBoundsException, SBMLException{
- if (node.getChildCount() == 0) {
- if (useId) {
- node.setType(ASTNode.Type.RELATIONAL_EQ);
- node.getChildren().clear();
- node.addChild(left);
- node.addChild(right);
- }
- else if (left.isNumber() && right.isNumber()) {
- if (left.getReal() == right.getReal()) {
- node.setValue(1);
- } else {
- node.setValue(0);
- }
- } else {
- throw new SBMLException();
- }
- return;
- }
- for (int i = 0; i < node.getChildCount(); ++i) {
- right.compile(this);
- ASTNode rightResult = getNode();
- left.compile(this);
- ASTNode leftResult = getNode();
- if (rightResult.isVector() && leftResult.isVector()) {
- eqRecursive(right.getChild(i),left.getChild(i), node.getChild(i));
- } else {
- throw new SBMLException();
- }
- }
- }
-
- /**
- *
- * @param vector
- * @param scalar
- */
- private void scalarVectorEq(ASTNode vector, ASTNode scalar) {
- for (int i = 0; i < vector.getChildCount(); ++i) {
- ASTNode child = vector.getChild(i);
- child.compile(this);
- ASTNode result = getNode();
- if (result.isVector()) {
- scalarVectorEq(child, scalar);
- } else if (useId) {
- vector.replaceChild(i, ASTNode.eq(result, scalar));
- } else if (result.isNumber() && scalar.isNumber()) {
- vector.getChild(i).setValue(result.getReal() == scalar.getReal() ? 1 : 0);
- } else {
- throw new SBMLException();
- }
- }
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.util.compilers.ASTNodeCompiler#exp(org.sbml.jsbml.ASTNode)
- */
- @Override
- public ASTNodeValue exp(ASTNode value) throws SBMLException {
- value.compile(this);
- ASTNode compiled = getNode();
- if (compiled.isVector()) {
- try {
- expRecursive(compiled);
- }
- catch(SBMLException e) {
- unknownValue();
- return dummy;
- }
- }
- else if (useId) {
- if (compiled.toString().equals("unknown")) {
- compiled.setName("unknown");
- } else {
- ASTNode nodeValue = new ASTNode(ASTNode.Type.FUNCTION_EXP, compiled.getParentSBMLObject());
- nodeValue.addChild(compiled);
- setNode(nodeValue);
- }
- return dummy;
- }
- else if (compiled.isNumber()) {
- compiled.setValue(Math.exp(compiled.getReal()));
- }
- else {
- compiled.setName("unknown");
- }
- setNode(compiled);
-
- return dummy;
- }
-
- /**
- * @param value
- */
- private void expRecursive(ASTNode value) {
- for (int i = 0; i < value.getChildCount(); i++) {
- value.getChild(i).compile(this);
- ASTNode child = getNode();
- if (child.isVector()) {
- expRecursive(value.getChild(i));
- }
- else if (useId){
- ASTNode expValue = new ASTNode(ASTNode.Type.FUNCTION_EXP, child.getParentSBMLObject());
- expValue.addChild(child.clone());
- value.replaceChild(i, expValue);
- }
- else if (child.isNumber()) {
- value.getChild(i).setValue(Math.exp(child.getReal()));
- }
- else {
- throw new SBMLException();
- }
- }
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.util.compilers.ASTNodeCompiler#factorial(org.sbml.jsbml.ASTNode)
- */
- @Override
- public ASTNodeValue factorial(ASTNode value) throws SBMLException {
- value.compile(this);
- ASTNode compiled = getNode();
- if (compiled.isVector()) {
- try {
- factorialRecursive(compiled);
- }
- catch(SBMLException e) {
- unknownValue();
- return dummy;
- }
- }
- else if (useId) {
- if (compiled.toString().equals("unknown")) {
- compiled.setName("unknown");
- } else {
- ASTNode nodeValue = new ASTNode(ASTNode.Type.FUNCTION_FACTORIAL, compiled.getParentSBMLObject());
- nodeValue.addChild(compiled);
- setNode(nodeValue);
- }
- return dummy;
- }
- else if (compiled.isNumber()) {
- double result = Maths.factorial(compiled.getInteger());
- compiled.setValue(result);
- }
- else {
- compiled = new ASTNode("unknown");
- }
-
- setNode(compiled);
- return dummy;
- }
-
- /**
- * @param value
- */
- private void factorialRecursive(ASTNode value) {
- for (int i = 0; i < value.getChildCount(); i++) {
- value.getChild(i).compile(this);
- ASTNode child = getNode();
- if (child.isVector()) {
- factorialRecursive(value.getChild(i));
- } else if (useId){
- ASTNode factValue = new ASTNode(ASTNode.Type.FUNCTION_FACTORIAL, child.getParentSBMLObject());
- factValue.addChild(child.clone());
- value.replaceChild(i, factValue);
- } else if (child.isNumber()) {
- value.getChild(i).setValue(Maths.factorial(child.getInteger()));
- } else {
- throw new SBMLException();
- }
- }
- }
- /* (non-Javadoc)
- * @see org.sbml.jsbml.util.compilers.ASTNodeCompiler#floor(org.sbml.jsbml.ASTNode)
- */
- @Override
- public ASTNodeValue floor(ASTNode value) throws SBMLException {
- value.compile(this);
- ASTNode compiled = getNode();
- if (compiled.isVector()) {
- try {
- floorRecursive(compiled);
- }
- catch(SBMLException e) {
- unknownValue();
- return dummy;
- }
- }
- else if (useId) {
- if (compiled.toString().equals("unknown")) {
- compiled.setName("unknown");
- } else {
- ASTNode nodeValue = new ASTNode(ASTNode.Type.FUNCTION_FLOOR, compiled.getParentSBMLObject());
- nodeValue.addChild(compiled);
- setNode(nodeValue);
- }
- return dummy;
- }
- else if (compiled.isNumber()) {
- compiled.setValue(Math.floor(compiled.getReal()));
- }
- else {
- compiled.setName("unknown");
- }
- setNode(compiled);
-
- return dummy;
- }
-
- /**
- * @param value
- */
- private void floorRecursive(ASTNode value) {
- for (int i = 0; i < value.getChildCount(); i++) {
- value.getChild(i).compile(this);
- ASTNode child = getNode();
- if (child.isVector()) {
- floorRecursive(value.getChild(i));
- } else if (useId){
- ASTNode floorValue = new ASTNode(ASTNode.Type.FUNCTION_FLOOR, child.getParentSBMLObject());
- floorValue.addChild(child.clone());
- value.replaceChild(i, floorValue);
- } else if (child.isNumber()) {
- value.getChild(i).setValue(Math.floor(child.getReal()));
- } else {
- throw new SBMLException();
- }
- }
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.util.compilers.ASTNodeCompiler#frac(org.sbml.jsbml.ASTNode, org.sbml.jsbml.ASTNode)
- */
- @Override
- public ASTNodeValue frac(ASTNode numerator, ASTNode denominator)
- throws SBMLException ...
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