Refactor: Move interfaces to their own package. Towards #7.

draeger-lab · Jun 6, 2016 · c9aa1ff · c9aa1ff
1 parent c7380a4
commit c9aa1ff
Show file tree

Hide file tree

Showing 14 changed files with 56 additions and 39 deletions.
diff --git a/src/main/java/edu/ucsd/sbrg/escher/models/AbstractBox.java b/src/main/java/edu/ucsd/sbrg/escher/models/AbstractBox.java
@@ -16,6 +16,8 @@
  */
 package edu.ucsd.sbrg.escher.models;
 
+import edu.ucsd.sbrg.escher.models.interfaces.Box;
+
 /**
  * @author Andreas Dr&auml;ger
  */
@@ -88,7 +90,7 @@ public boolean equals(Object obj) {
 
 
   /* (non-Javadoc)
-   * @see edu.ucsd.sbrg.escher.models.Box#getHeight()
+   * @see edu.ucsd.sbrg.escher.models.interfaces.Box#getHeight()
    */
   @Override
   public Double getHeight() {
@@ -97,7 +99,7 @@ public Double getHeight() {
 
 
   /* (non-Javadoc)
-   * @see edu.ucsd.sbrg.escher.models.Box#getWidth()
+   * @see edu.ucsd.sbrg.escher.models.interfaces.Box#getWidth()
    */
   @Override
   public Double getWidth() {
@@ -119,7 +121,7 @@ public int hashCode() {
 
 
   /* (non-Javadoc)
-   * @see edu.ucsd.sbrg.escher.models.Box#isSetHeight()
+   * @see edu.ucsd.sbrg.escher.models.interfaces.Box#isSetHeight()
    */
   @Override
   public boolean isSetHeight() {
@@ -128,7 +130,7 @@ public boolean isSetHeight() {
 
 
   /* (non-Javadoc)
-   * @see edu.ucsd.sbrg.escher.models.Box#isSetWidth()
+   * @see edu.ucsd.sbrg.escher.models.interfaces.Box#isSetWidth()
    */
   @Override
   public boolean isSetWidth() {
@@ -137,7 +139,7 @@ public boolean isSetWidth() {
 
 
   /* (non-Javadoc)
-   * @see edu.ucsd.sbrg.escher.models.Box#setHeight(java.lang.Double)
+   * @see edu.ucsd.sbrg.escher.models.interfaces.Box#setHeight(java.lang.Double)
    */
   @Override
   public void setHeight(Double height) {
@@ -146,7 +148,7 @@ public void setHeight(Double height) {
 
 
   /* (non-Javadoc)
-   * @see edu.ucsd.sbrg.escher.models.Box#setWidth(java.lang.Double)
+   * @see edu.ucsd.sbrg.escher.models.interfaces.Box#setWidth(java.lang.Double)
    */
   @Override
   public void setWidth(Double width) {

diff --git a/src/main/java/edu/ucsd/sbrg/escher/models/AbstractEscherBase.java b/src/main/java/edu/ucsd/sbrg/escher/models/AbstractEscherBase.java
@@ -16,6 +16,8 @@
  */
 package edu.ucsd.sbrg.escher.models;
 
+import edu.ucsd.sbrg.escher.models.interfaces.EscherBase;
+
 import java.util.HashMap;
 import java.util.Map;
 import java.util.Set;
@@ -82,7 +84,7 @@ public boolean equals(Object obj) {
 
 
   /* (non-Javadoc)
-   * @see edu.ucsd.sbrg.escher.models.EscherBase#getUserObject(java.lang.String)
+   * @see edu.ucsd.sbrg.escher.models.interfaces.EscherBase#getUserObject(java.lang.String)
    */
   @Override
   public Object getUserObject(String key) {
@@ -104,7 +106,7 @@ public int hashCode() {
 
 
   /* (non-Javadoc)
-   * @see edu.ucsd.sbrg.escher.models.EscherBase#putUserObject(java.lang.String, T)
+   * @see edu.ucsd.sbrg.escher.models.interfaces.EscherBase#putUserObject(java.lang.String, T)
    */
   @Override
   public <T> Object putUserObject(String key, T value) {
@@ -113,7 +115,7 @@ public <T> Object putUserObject(String key, T value) {
 
 
   /* (non-Javadoc)
-   * @see edu.ucsd.sbrg.escher.models.EscherBase#userObjectEntrySet()
+   * @see edu.ucsd.sbrg.escher.models.interfaces.EscherBase#userObjectEntrySet()
    */
   @Override
   public Set<Map.Entry<String, Object>> userObjectEntrySet() {
@@ -122,7 +124,7 @@ public Set<Map.Entry<String, Object>> userObjectEntrySet() {
 
 
   /* (non-Javadoc)
-   * @see edu.ucsd.sbrg.escher.models.EscherBase#userObjectKeys()
+   * @see edu.ucsd.sbrg.escher.models.interfaces.EscherBase#userObjectKeys()
    */
   @Override
   public Set<String> userObjectKeys() {

diff --git a/src/main/java/edu/ucsd/sbrg/escher/models/AbstractPosition.java b/src/main/java/edu/ucsd/sbrg/escher/models/AbstractPosition.java
@@ -16,6 +16,8 @@
  */
 package edu.ucsd.sbrg.escher.models;
 
+import edu.ucsd.sbrg.escher.models.interfaces.Position;
+
 /**
  * @author Andreas Dr&auml;ger
  */
@@ -100,7 +102,7 @@ public boolean equals(Object obj) {
 
 
   /* (non-Javadoc)
-   * @see edu.ucsd.sbrg.escher.models.Position#getX()
+   * @see edu.ucsd.sbrg.escher.models.interfaces.Position#getX()
    */
   @Override
   public Double getX() {
@@ -109,7 +111,7 @@ public Double getX() {
 
 
   /* (non-Javadoc)
-   * @see edu.ucsd.sbrg.escher.models.Position#getY()
+   * @see edu.ucsd.sbrg.escher.models.interfaces.Position#getY()
    */
   @Override
   public Double getY() {
@@ -131,7 +133,7 @@ public int hashCode() {
 
 
   /* (non-Javadoc)
-   * @see edu.ucsd.sbrg.escher.models.Position#isSetX()
+   * @see edu.ucsd.sbrg.escher.models.interfaces.Position#isSetX()
    */
   @Override
   public boolean isSetX() {
@@ -140,7 +142,7 @@ public boolean isSetX() {
 
 
   /* (non-Javadoc)
-   * @see edu.ucsd.sbrg.escher.models.Position#isSetY()
+   * @see edu.ucsd.sbrg.escher.models.interfaces.Position#isSetY()
    */
   @Override
   public boolean isSetY() {
@@ -149,7 +151,7 @@ public boolean isSetY() {
 
 
   /* (non-Javadoc)
-   * @see edu.ucsd.sbrg.escher.models.Position#setX(java.lang.Double)
+   * @see edu.ucsd.sbrg.escher.models.interfaces.Position#setX(java.lang.Double)
    */
   @Override
   public void setX(Double x) {
@@ -158,7 +160,7 @@ public void setX(Double x) {
 
 
   /* (non-Javadoc)
-   * @see edu.ucsd.sbrg.escher.models.Position#setY(java.lang.Double)
+   * @see edu.ucsd.sbrg.escher.models.interfaces.Position#setY(java.lang.Double)
    */
   @Override
   public void setY(Double y) {

diff --git a/src/main/java/edu/ucsd/sbrg/escher/models/EscherCompartment.java b/src/main/java/edu/ucsd/sbrg/escher/models/EscherCompartment.java
@@ -16,6 +16,7 @@
  */
 package edu.ucsd.sbrg.escher.models;
 
+import edu.ucsd.sbrg.escher.models.interfaces.Element;
 import org.sbml.jsbml.util.ResourceManager;
 
 import java.text.MessageFormat;
@@ -79,7 +80,7 @@ public EscherCompartment clone() {
 
 
   /* (non-Javadoc)
-   * @see edu.ucsd.sbrg.escher.models.Element#getId()
+   * @see edu.ucsd.sbrg.escher.models.interfaces.Element#getId()
    */
   @Override
   public String getId() {
@@ -99,7 +100,7 @@ public String getName() {
 
 
   /* (non-Javadoc)
-   * @see edu.ucsd.sbrg.escher.models.Element#isSetId()
+   * @see edu.ucsd.sbrg.escher.models.interfaces.Element#isSetId()
    */
   @Override
   public boolean isSetId() {
@@ -116,7 +117,7 @@ public boolean isSetName() {
 
 
   /* (non-Javadoc)
-   * @see edu.ucsd.sbrg.escher.models.Element#setId(java.lang.String)
+   * @see edu.ucsd.sbrg.escher.models.interfaces.Element#setId(java.lang.String)
    */
   @Override
   public void setId(String id) {

diff --git a/src/main/java/edu/ucsd/sbrg/escher/models/EscherReaction.java b/src/main/java/edu/ucsd/sbrg/escher/models/EscherReaction.java
@@ -16,6 +16,7 @@
  */
 package edu.ucsd.sbrg.escher.models;
 
+import edu.ucsd.sbrg.escher.models.interfaces.Element;
 import org.sbml.jsbml.util.ResourceManager;
 
 import java.text.MessageFormat;
@@ -362,7 +363,7 @@ public Map<String, Gene> getGenes() {
 
 
   /* (non-Javadoc)
-   * @see edu.ucsd.sbrg.escher.models.Element#getId()
+   * @see edu.ucsd.sbrg.escher.models.interfaces.Element#getId()
    */
   @Override
   public String getId() {
@@ -511,7 +512,7 @@ public boolean isSetGeneReactionRule() {
 
 
   /* (non-Javadoc)
-   * @see edu.ucsd.sbrg.escher.models.Element#isSetId()
+   * @see edu.ucsd.sbrg.escher.models.interfaces.Element#isSetId()
    */
   @Override
   public boolean isSetId() {
@@ -593,7 +594,7 @@ public void setGeneReactionRule(String geneReactionRule) {
 
 
   /* (non-Javadoc)
-   * @see edu.ucsd.sbrg.escher.models.Element#setId(java.lang.String)
+   * @see edu.ucsd.sbrg.escher.models.interfaces.Element#setId(java.lang.String)
    */
   @Override
   public void setId(String id) {

diff --git a/src/main/java/edu/ucsd/sbrg/escher/models/Gene.java b/src/main/java/edu/ucsd/sbrg/escher/models/Gene.java
@@ -16,6 +16,8 @@
  */
 package edu.ucsd.sbrg.escher.models;
 
+import edu.ucsd.sbrg.escher.models.interfaces.Element;
+
 /**
  * @author Andreas Dr&auml;ger
  */
@@ -102,7 +104,7 @@ public boolean equals(Object obj) {
 
 
   /* (non-Javadoc)
-   * @see edu.ucsd.sbrg.escher.models.Element#getId()
+   * @see edu.ucsd.sbrg.escher.models.interfaces.Element#getId()
    */
   @Override
   public String getId() {
@@ -132,7 +134,7 @@ public int hashCode() {
 
 
   /* (non-Javadoc)
-   * @see edu.ucsd.sbrg.escher.models.Element#isSetId()
+   * @see edu.ucsd.sbrg.escher.models.interfaces.Element#isSetId()
    */
   @Override
   public boolean isSetId() {
@@ -149,7 +151,7 @@ public boolean isSetName() {
 
 
   /* (non-Javadoc)
-   * @see edu.ucsd.sbrg.escher.models.Element#setId(java.lang.String)
+   * @see edu.ucsd.sbrg.escher.models.interfaces.Element#setId(java.lang.String)
    */
   @Override
   public void setId(String id) {

diff --git a/src/main/java/edu/ucsd/sbrg/escher/models/Metabolite.java b/src/main/java/edu/ucsd/sbrg/escher/models/Metabolite.java
@@ -16,6 +16,8 @@
  */
 package edu.ucsd.sbrg.escher.models;
 
+import edu.ucsd.sbrg.escher.models.interfaces.Element;
+
 /**
  * @author Andreas Dr&auml;ger
  */
@@ -119,7 +121,7 @@ public Double getCoefficient() {
 
 
   /* (non-Javadoc)
-   * @see edu.ucsd.sbrg.escher.models.Element#getId()
+   * @see edu.ucsd.sbrg.escher.models.interfaces.Element#getId()
    */
   @Override
   public String getId() {
@@ -159,7 +161,7 @@ public boolean isSetCoefficient() {
 
 
   /* (non-Javadoc)
-   * @see edu.ucsd.sbrg.escher.models.Element#isSetId()
+   * @see edu.ucsd.sbrg.escher.models.interfaces.Element#isSetId()
    */
   @Override
   public boolean isSetId() {
@@ -184,7 +186,7 @@ public void setCoefficient(Double coefficient) {
 
 
   /* (non-Javadoc)
-   * @see edu.ucsd.sbrg.escher.models.Element#setId(java.lang.String)
+   * @see edu.ucsd.sbrg.escher.models.interfaces.Element#setId(java.lang.String)
    */
   @Override
   public void setId(String id) {

diff --git a/src/main/java/edu/ucsd/sbrg/escher/models/Node.java b/src/main/java/edu/ucsd/sbrg/escher/models/Node.java
@@ -16,6 +16,7 @@
  */
 package edu.ucsd.sbrg.escher.models;
 
+import edu.ucsd.sbrg.escher.models.interfaces.Element;
 import org.sbml.jsbml.util.ResourceManager;
 
 import java.text.MessageFormat;
@@ -557,7 +558,7 @@ public void setConnectedSegments(
 
 
   /* (non-Javadoc)
-   * @see edu.ucsd.sbrg.escher.models.Element#setId(java.lang.String)
+   * @see edu.ucsd.sbrg.escher.models.interfaces.Element#setId(java.lang.String)
    */
   @Override
   public void setId(String id) {

diff --git a/src/main/java/edu/ucsd/sbrg/escher/models/Segment.java b/src/main/java/edu/ucsd/sbrg/escher/models/Segment.java
@@ -16,6 +16,8 @@
  */
 package edu.ucsd.sbrg.escher.models;
 
+import edu.ucsd.sbrg.escher.models.interfaces.Element;
+
 /**
  * @author Andreas Dr&auml;ger
  */
@@ -163,7 +165,7 @@ public String getFromNodeId() {
 
 
   /* (non-Javadoc)
-   * @see edu.ucsd.sbrg.escher.models.Element#getId()
+   * @see edu.ucsd.sbrg.escher.models.interfaces.Element#getId()
    */
   @Override
   public String getId() {
@@ -221,7 +223,7 @@ public boolean isSetFromNodeId() {
 
 
   /* (non-Javadoc)
-   * @see edu.ucsd.sbrg.escher.models.Element#isSetId()
+   * @see edu.ucsd.sbrg.escher.models.interfaces.Element#isSetId()
    */
   @Override
   public boolean isSetId() {
@@ -282,7 +284,7 @@ public void setFromNodeId(String fromNodeId) {
 
 
   /* (non-Javadoc)
-   * @see edu.ucsd.sbrg.escher.models.Element#setId(java.lang.String)
+   * @see edu.ucsd.sbrg.escher.models.interfaces.Element#setId(java.lang.String)
    */
   @Override
   public void setId(String id) {