Menu
▾
▴
[Jsbml-svn] SF.net SVN: jsbml:[2268] branches/astnode2-merging-alternate/extensions/ spatial/src/org/sbml/jsbml/ext/spatial
|
From: <nik...@us...> - 2015-05-01 09:46:02
|
Revision: 2268
http://sourceforge.net/p/jsbml/code/2268
Author: niko-rodrigue
Date: 2015-05-01 09:46:00 +0000 (Fri, 01 May 2015)
Log Message:
-----------
merged from trunk until rev 2217
Revision Links:
--------------
http://sourceforge.net/p/jsbml/code/2217
Removed Paths:
-------------
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ImageData.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoint.java
Deleted: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ImageData.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ImageData.java 2015-05-01 09:44:19 UTC (rev 2267)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ImageData.java 2015-05-01 09:46:00 UTC (rev 2268)
@@ -1,358 +0,0 @@
-/*
- * $Id$
- * $URL$
- * ----------------------------------------------------------------------------
- * 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
- *
- * 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.spatial;
-
-import java.text.MessageFormat;
-import java.util.Arrays;
-import java.util.Map;
-import java.util.StringTokenizer;
-
-import org.sbml.jsbml.AbstractSBase;
-import org.sbml.jsbml.PropertyUndefinedError;
-import org.sbml.jsbml.util.StringTools;
-
-/**
- * @author Alex Thomas
- * @author Andreas Dräger
- * @since 1.0
- * @version $Rev$
- */
-public class ImageData extends AbstractSBase {
-
- /**
- * Generated serial version identifier.
- */
- private static final long serialVersionUID = 1872012239027099782L;
-
- /**
- *
- */
- private Integer samplesLength;
- /**
- *
- */
- private Integer samples[];
-
- /**
- *
- */
- private String dataType;
-
- /**
- *
- */
- public ImageData() {
- super();
- initDefaults();
- }
-
- /**
- * @param im
- */
- public ImageData(ImageData im) {
- super(im);
- if (im.isSetSamples()) {
- samples = im.getSamples().clone();
- samplesLength = samples.length;
- }
- if (im.isSetDataType()) {
- dataType = new String(im.getDataType());
- }
- }
-
- /**
- * @param level
- * @param version
- */
- public ImageData(int level, int version) {
- super(level, version);
- initDefaults();
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.AbstractSBase#clone()
- */
- @Override
- public ImageData clone() {
- return new ImageData(this);
- }
-
- /**
- * Initializes the default values using the namespace.
- */
- public void initDefaults() {
- setNamespace(SpatialConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
- setPackageVersion(-1);
- packageName = SpatialConstants.shortLabel;
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.AbstractSBase#equals(java.lang.Object)
- */
- @Override
- public boolean equals(Object object) {
- boolean equal = super.equals(object);
- if (equal) {
- ImageData im = (ImageData) object;
-
- equal &= im.isSetSamples() == isSetSamples();
- if (equal && isSetSamples()) {
- equal &= im.getSamples().equals(getSamples());
- }
-
- equal &= im.isSetDataType() == isSetDataType();
- if (equal && isSetDataType()) {
- equal &= im.getDataType().equals(getDataType());
- }
-
- }
- return equal;
- }
-
-
- /**
- * Returns the value of samples
- *
- * @return the value of samples
- */
- public Integer[] getSamples() {
- if (isSetSamples()) {
- return samples;
- }
- // This is necessary if we cannot return null here.
- throw new PropertyUndefinedError(SpatialConstants.samples, this);
- }
-
-
- /**
- * Returns whether samples is set
- *
- * @return whether samples is set
- */
- public boolean isSetSamples() {
- return samples != null;
- }
-
- /**
- * Sets the value of samples
- * @param samples
- */
- public void setSamples(Integer... samples) {
- Integer[] oldSamples = this.samples;
- this.samples = samples;
- samplesLength = samples.length;
- firePropertyChange(SpatialConstants.samples, oldSamples, this.samples);
- firePropertyChange(SpatialConstants.samples, oldSamples.length, samplesLength);
- }
-
- /**
- * Unsets the variable samples
- *
- * @return {@code true}, if samples was set before,
- * otherwise {@code false}
- */
- public boolean unsetSamples() {
- if (isSetSamples()) {
- Integer[] oldSamples = samples;
- samples = null;
- samplesLength = null;
- firePropertyChange(SpatialConstants.samples, oldSamples, samples);
- firePropertyChange(SpatialConstants.samplesLength, oldSamples.length, samplesLength);
- return true;
- }
- return false;
- }
-
-
- /**
- * Returns the value of samplesLength
- *
- * @return the value of samplesLength
- */
- public int getSamplesLength() {
- if (isSetSamplesLength()) {
- return samplesLength;
- }
- // This is necessary if we cannot return null here.
- throw new PropertyUndefinedError(SpatialConstants.samplesLength, this);
- }
-
-
- /**
- * Returns whether samplesLength is set
- *
- * @return whether samplesLength is set
- */
- public boolean isSetSamplesLength() {
- return samplesLength != null;
- }
-
-
- /**
- * Returns the value of dataType
- *
- * @return the value of dataType
- */
- public String getDataType() {
- if (isSetDataType()) {
- return dataType;
- }
- return null;
- }
-
-
- /**
- * Returns whether dataType is set
- *
- * @return whether dataType is set
- */
- public boolean isSetDataType() {
- return dataType != null;
- }
-
- /**
- * Sets the value of dataType
- * @param dataType
- */
- public void setDataType(String dataType) {
- String oldDataType = this.dataType;
- this.dataType = dataType;
- firePropertyChange(SpatialConstants.dataType, oldDataType, this.dataType);
- }
-
- /**
- * Unsets the variable dataType
- *
- * @return {@code true}, if dataType was set before,
- * otherwise {@code false}
- */
- public boolean unsetDataType() {
- if (isSetDataType()) {
- String oldDataType = dataType;
- dataType = null;
- firePropertyChange(SpatialConstants.dataType, oldDataType, dataType);
- return true;
- }
- return false;
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.AbstractSBase#hashCode()
- */
- @Override
- public int hashCode() {
- final int prime = 983;//Change this prime number
- int hashCode = super.hashCode();
- if (isSetSamples()) {
- hashCode += prime * getSamples().hashCode();
- }
- if (isSetDataType()) {
- hashCode += prime * getDataType().hashCode();
- }
-
- return hashCode;
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.AbstractSBase#writeXMLAttributes()
- */
- @Override
- public Map<String, String> writeXMLAttributes() {
- Map<String, String> attributes = super.writeXMLAttributes();
- if (isSetSamples()) {
- attributes.remove("samples");
- attributes.put(SpatialConstants.shortLabel + ":samples", Arrays.toString(getSamples()));
- }
-
- if (isSetSamplesLength()) {
- attributes.remove("samplesLength");
- attributes.put(SpatialConstants.shortLabel + ":samplesLength",
- String.valueOf(getSamplesLength()));
- }
-
- if (isSetDataType()) {
- attributes.remove("dataType");
- attributes.put(SpatialConstants.shortLabel + ":dataType",
- getDataType());
- }
- return attributes;
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.AbstractSBase#readAttribute(java.lang.String, java.lang.String, java.lang.String)
- */
- @Override
- public boolean readAttribute(String attributeName, String prefix, String value) {
- boolean isAttributeRead = (super.readAttribute(attributeName, prefix, value))
- && (SpatialConstants.shortLabel == prefix);
- if (!isAttributeRead) {
- isAttributeRead = true;
- if (attributeName.equals(SpatialConstants.samples)) {
- StringTokenizer test = new StringTokenizer(value);
- Integer[] samplesTemp = new Integer[test.countTokens()];
- int i = 0;
- while(test.hasMoreTokens()) {
- try {
- samplesTemp[i] = StringTools.parseSBMLInt(test.nextToken());
- i++;
- } catch (Exception e) {
- MessageFormat.format(
- SpatialConstants.bundle.getString("COULD_NOT_READ"), value,
- SpatialConstants.pointIndex);
- }
- }
- if (samplesTemp.length > 0) {
- unsetSamples();
- setSamples(samplesTemp);
- }
- }
- else if (attributeName.equals(SpatialConstants.dataType)) {
- try {
- setDataType(value);
- } catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.dataType);
- }
- }
- else {
- isAttributeRead = false;
- }
- }
- return isAttributeRead;
- }
-
- /* (non-Javadoc)
- * @see java.lang.Object#toString()
- */
- @Override
- public String toString() {
- StringBuilder builder = new StringBuilder();
- builder.append("ImageData [samplesLength=");
- builder.append(samplesLength);
- builder.append(", dataType=");
- builder.append(dataType);
- builder.append(", samples=");
- builder.append(Arrays.toString(samples)); // TODO - Should we really print the whole content of the array here?
- builder.append("]");
- return builder.toString();
- }
-
-}
Deleted: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoint.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoint.java 2015-05-01 09:44:19 UTC (rev 2267)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoint.java 2015-05-01 09:46:00 UTC (rev 2268)
@@ -1,468 +0,0 @@
-/*
- * $Id$
- * $URL$
- * ----------------------------------------------------------------------------
- * 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
- *
- * 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.spatial;
-
-import java.text.MessageFormat;
-import java.util.Map;
-
-import org.sbml.jsbml.PropertyUndefinedError;
-import org.sbml.jsbml.util.StringTools;
-
-/**
- * @author Alex Thomas
- * @author Andreas Dräger
- * @since 1.0
- * @version $Rev$
- */
-public class SpatialPoint extends AbstractSpatialNamedSBase {
-
- /**
- *
- */
- private String domain;
-
- /**
- *
- */
- private Double coord1;
- /**
- *
- */
- private Double coord2;
- /**
- *
- */
- private Double coord3;
-
- /**
- * Generated serial version identifier.
- */
- private static final long serialVersionUID = -1171421071571874086L;
-
- /**
- *
- */
- public SpatialPoint() {
- super();
- }
-
- /**
- * @param sp
- */
- public SpatialPoint(SpatialPoint sp) {
- super(sp);
-
-
- if (sp.isSetDomain()) {
- domain = new String(sp.getDomain());
- }
-
- if (sp.isSetCoord1()) {
- coord1 = new Double(sp.getCoord1());
- }
-
- if (sp.isSetCoord2()) {
- coord2 = new Double(sp.getCoord2());
- }
-
- if (sp.isSetCoord3()) {
- coord3 = new Double(sp.getCoord3());
- }
- }
-
-
- /**
- * @param level
- * @param version
- */
- public SpatialPoint(int level, int version) {
- super(level, version);
- }
-
-
- /**
- *
- * @param id
- * @param level
- * @param version
- */
- public SpatialPoint(String id, int level, int version) {
- super(id, level, version);
- }
-
-
- @Override
- public SpatialPoint clone() {
- return new SpatialPoint(this);
- }
-
-
- @Override
- public boolean equals(Object object) {
- boolean equal = super.equals(object);
- if (equal) {
- SpatialPoint sp = (SpatialPoint) object;
-
- equal &= sp.isSetDomain() == isSetDomain();
- if (equal && isSetDomain()) {
- equal &= sp.getDomain().equals(getDomain());
- }
-
- equal &= sp.isSetCoord1() == isSetCoord1();
- if (equal && isSetCoord1()) {
- equal &= sp.getCoord1() == getCoord1();
- }
-
- equal &= sp.isSetCoord2() == isSetCoord2();
- if (equal && isSetCoord2()) {
- equal &= sp.getCoord2() == getCoord2();
- }
-
- equal &= sp.isSetCoord3() == isSetCoord3();
- if (equal && isSetCoord3()) {
- equal &= sp.getCoord3() == getCoord3();
- }
- //TODO: add equal statements for each attribute and class
- }
- return equal;
- }
-
- /**
- * Returns the value of coord1
- *
- * @return the value of coord1
- */
- public double getCoord1() {
- if (isSetCoord1()) {
- return coord1;
- }
- //TODO: This is necessary if we cannot return null here.
- throw new PropertyUndefinedError(SpatialConstants.coord1, this);
- }
-
-
- /**
- * Returns whether coord1 is set
- *
- * @return whether coord1 is set
- */
- public boolean isSetCoord1() {
- return coord1 != null;
- }
-
- /**
- * Sets the value of coord1
- * @param coord1
- */
- public void setCoord1(double coord1) {
- double oldCoord1 = this.coord1;
- this.coord1 = coord1;
- firePropertyChange(SpatialConstants.coord1, oldCoord1, this.coord1);
- }
-
-
- /**
- * Unsets the variable coord1
- *
- * @return {@code true}, if coord1 was set before,
- * otherwise {@code false}
- */
- public boolean unsetCoord1() {
- if (isSetCoord1()) {
- double oldCoord1 = coord1;
- coord1 = null;
- firePropertyChange(SpatialConstants.coord1, oldCoord1, coord1);
- return true;
- }
- return false;
- }
-
- /**
- * Returns the value of coord2
- *
- * @return the value of coord2
- */
- public double getCoord2() {
- if (isSetCoord2()) {
- return coord2;
- }
- //TODO: This is necessary if we cannot return null here.
- throw new PropertyUndefinedError(SpatialConstants.coord2, this);
- }
-
-
- /**
- * Returns whether coord2 is set
- *
- * @return whether coord2 is set
- */
- public boolean isSetCoord2() {
- return coord2 != null;
- }
-
- /**
- * Sets the value of coord2
- * @param coord2
- */
- public void setCoord2(double coord2) {
- double oldCoord2 = this.coord2;
- this.coord2 = coord2;
- firePropertyChange(SpatialConstants.coord2, oldCoord2, this.coord2);
- }
-
-
- /**
- * Unsets the variable coord2
- *
- * @return {@code true}, if coord2 was set before,
- * otherwise {@code false}
- */
- public boolean unsetCoord2() {
- if (isSetCoord2()) {
- double oldCoord2 = coord2;
- coord2 = null;
- firePropertyChange(SpatialConstants.coord2, oldCoord2, coord2);
- return true;
- }
- return false;
- }
-
- /**
- * Returns the value of coord3
- *
- * @return the value of coord3
- */
- public double getCoord3() {
- if (isSetCoord3()) {
- return coord3;
- }
- // TODO:This is necessary if we cannot return null here.
- throw new PropertyUndefinedError(SpatialConstants.coord3, this);
- }
-
-
- /**
- * Returns whether coord3 is set
- *
- * @return whether coord3 is set
- */
- public boolean isSetCoord3() {
- return coord3 != null;
- }
-
- /**
- * Sets the value of coord3
- * @param coord3
- */
- public void setCoord3(double coord3) {
- double oldCoord3 = this.coord3;
- this.coord3 = coord3;
- firePropertyChange(SpatialConstants.coord3, oldCoord3, this.coord3);
- }
-
-
- /**
- * Unsets the variable coord3
- *
- * @return {@code true}, if coord3 was set before,
- * otherwise {@code false}
- */
- public boolean unsetCoord3() {
- if (isSetCoord3()) {
- double oldCoord3 = coord3;
- coord3 = null;
- firePropertyChange(SpatialConstants.coord3, oldCoord3, coord3);
- return true;
- }
- return false;
- }
-
- /**
- * Returns the value of domain
- *
- * @return the value of domain
- */
- public String getDomain() {
- if (isSetDomain()) {
- return domain;
- }
- // TODO: This is necessary if we cannot return null here.
- throw new PropertyUndefinedError(SpatialConstants.domain, this);
- }
-
-
- /**
- * Returns whether domain is set
- *
- * @return whether domain is set
- */
- public boolean isSetDomain() {
- return domain != null;
- }
-
- /**
- * Sets the value of domain
- * @param domain
- */
- public void setDomain(String domain) {
- String oldDomain = this.domain;
- this.domain = domain;
- firePropertyChange(SpatialConstants.domain, oldDomain, this.domain);
- }
-
- /**
- * Unsets the variable domain
- *
- * @return {@code true}, if domain was set before,
- * otherwise {@code false}
- */
- public boolean unsetDomain() {
- if (isSetDomain()) {
- String oldDomain = domain;
- domain = null;
- firePropertyChange(SpatialConstants.domain, oldDomain, domain);
- return true;
- }
- return false;
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase#hashCode()
- */
- @Override
- public int hashCode() {
- final int prime = 983;//Change this prime number
- int hashCode = super.hashCode();
- if (isSetDomain()) {
- hashCode += prime * getDomain().hashCode();
- }
-
- if (isSetCoord1()) {
- hashCode += prime * getCoord1();
- }
-
- if (isSetCoord2()) {
- hashCode += prime * getCoord2();
- }
-
- if (isSetCoord3()) {
- hashCode += prime * getCoord3();
- }
- return hashCode;
- }
-
-
- @Override
- public Map<String, String> writeXMLAttributes() {
- Map<String, String> attributes = super.writeXMLAttributes();
- if (isSetDomain()) {
- attributes.remove("domain");
- attributes.put(SpatialConstants.shortLabel + ":domain", getDomain());
- }
-
- if (isSetCoord1()) {
- attributes.remove("coord1");
- attributes.put(SpatialConstants.shortLabel + ":coord1",
- String.valueOf(getCoord1()));
- }
-
- if (isSetCoord2()) {
- attributes.remove("coord1");
- attributes.put(SpatialConstants.shortLabel + ":coord1",
- String.valueOf(getCoord2()));
- }
-
- if (isSetCoord3()) {
- attributes.remove("coord3");
- attributes.put(SpatialConstants.shortLabel + ":coord3",
- String.valueOf(getCoord3()));
- }
- return attributes;
- }
-
-
- @Override
- public boolean readAttribute(String attributeName, String prefix, String value) {
- boolean isAttributeRead = (super.readAttribute(attributeName, prefix, value))
- && (SpatialConstants.shortLabel == prefix);
- if (!isAttributeRead) {
- isAttributeRead = true;
- if (attributeName.equals(SpatialConstants.domain)) {
- try {
- setDomain(value);
- } catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value,
- SpatialConstants.domain);
- }
- }
-
- else if (attributeName.equals(SpatialConstants.coord1)) {
- try {
- setCoord1(StringTools.parseSBMLDouble(value));
- } catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.coord1);
- }
- }
-
- else if (attributeName.equals(SpatialConstants.coord2)) {
- try {
- setCoord2(StringTools.parseSBMLDouble(value));
- } catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.coord2);
- }
- }
-
- else if (attributeName.equals(SpatialConstants.coord3)) {
- try {
- setCoord3(StringTools.parseSBMLDouble(value));
- } catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.coord3);
- }
- }
- else {
- isAttributeRead = false;
- }
- }
- return isAttributeRead;
- }
-
- /* (non-Javadoc)
- * @see java.lang.Object#toString()
- */
- @Override
- public String toString() {
- StringBuilder builder = new StringBuilder();
- builder.append("SpatialPoint [domain=");
- builder.append(domain);
- builder.append(", coord1=");
- builder.append(coord1);
- builder.append(", coord2=");
- builder.append(coord2);
- builder.append(", coord3=");
- builder.append(coord3);
- builder.append("]");
- return builder.toString();
- }
-
-
-
-}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
