X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FJSeq.java;h=ee559455cd465b7c4dbb275e78380841a7f9c497;hb=0fc704a18faa7d11b6d02876bb6c1e8bc19f343c;hp=751409f0b161223878e176c9ab5f6389894670bc;hpb=c68ce4c63bd79f23b87aac3eb0afa7f6b42a3098;p=jalview.git

diff --git a/src/jalview/binding/JSeq.java b/src/jalview/binding/JSeq.java
index 751409f..ee55945 100755
--- a/src/jalview/binding/JSeq.java
+++ b/src/jalview/binding/JSeq.java
@@ -15,6 +15,8 @@ import java.io.IOException;
 import java.io.Reader;
 import java.io.Serializable;
 import java.io.Writer;
+import java.util.Enumeration;
+import java.util.Vector;
 import org.exolab.castor.xml.MarshalException;
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -73,6 +75,16 @@ public class JSeq implements java.io.Serializable {
      */
     private boolean _has_id;
 
+    /**
+     * Field _featuresList
+     */
+    private java.util.Vector _featuresList;
+
+    /**
+     * Field _pdbidsList
+     */
+    private java.util.Vector _pdbidsList;
+
 
       //----------------/
      //- Constructors -/
@@ -80,6 +92,8 @@ public class JSeq implements java.io.Serializable {
 
     public JSeq() {
         super();
+        _featuresList = new Vector();
+        _pdbidsList = new Vector();
     } //-- jalview.binding.JSeq()
 
 
@@ -88,6 +102,60 @@ public class JSeq implements java.io.Serializable {
     //-----------/
 
     /**
+     * Method addFeatures
+     * 
+     * 
+     * 
+     * @param vFeatures
+     */
+    public void addFeatures(jalview.binding.Features vFeatures)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _featuresList.addElement(vFeatures);
+    } //-- void addFeatures(jalview.binding.Features) 
+
+    /**
+     * Method addFeatures
+     * 
+     * 
+     * 
+     * @param index
+     * @param vFeatures
+     */
+    public void addFeatures(int index, jalview.binding.Features vFeatures)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _featuresList.insertElementAt(vFeatures, index);
+    } //-- void addFeatures(int, jalview.binding.Features) 
+
+    /**
+     * Method addPdbids
+     * 
+     * 
+     * 
+     * @param vPdbids
+     */
+    public void addPdbids(jalview.binding.Pdbids vPdbids)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _pdbidsList.addElement(vPdbids);
+    } //-- void addPdbids(jalview.binding.Pdbids) 
+
+    /**
+     * Method addPdbids
+     * 
+     * 
+     * 
+     * @param index
+     * @param vPdbids
+     */
+    public void addPdbids(int index, jalview.binding.Pdbids vPdbids)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _pdbidsList.insertElementAt(vPdbids, index);
+    } //-- void addPdbids(int, jalview.binding.Pdbids) 
+
+    /**
      * Method deleteColour
      * 
      */
@@ -124,6 +192,30 @@ public class JSeq implements java.io.Serializable {
     } //-- void deleteStart() 
 
     /**
+     * Method enumerateFeatures
+     * 
+     * 
+     * 
+     * @return Enumeration
+     */
+    public java.util.Enumeration enumerateFeatures()
+    {
+        return _featuresList.elements();
+    } //-- java.util.Enumeration enumerateFeatures() 
+
+    /**
+     * Method enumeratePdbids
+     * 
+     * 
+     * 
+     * @return Enumeration
+     */
+    public java.util.Enumeration enumeratePdbids()
+    {
+        return _pdbidsList.elements();
+    } //-- java.util.Enumeration enumeratePdbids() 
+
+    /**
      * Returns the value of field 'colour'.
      * 
      * @return int
@@ -146,6 +238,54 @@ public class JSeq implements java.io.Serializable {
     } //-- int getEnd() 
 
     /**
+     * Method getFeatures
+     * 
+     * 
+     * 
+     * @param index
+     * @return Features
+     */
+    public jalview.binding.Features getFeatures(int index)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _featuresList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        
+        return (jalview.binding.Features) _featuresList.elementAt(index);
+    } //-- jalview.binding.Features getFeatures(int) 
+
+    /**
+     * Method getFeatures
+     * 
+     * 
+     * 
+     * @return Features
+     */
+    public jalview.binding.Features[] getFeatures()
+    {
+        int size = _featuresList.size();
+        jalview.binding.Features[] mArray = new jalview.binding.Features[size];
+        for (int index = 0; index < size; index++) {
+            mArray[index] = (jalview.binding.Features) _featuresList.elementAt(index);
+        }
+        return mArray;
+    } //-- jalview.binding.Features[] getFeatures() 
+
+    /**
+     * Method getFeaturesCount
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int getFeaturesCount()
+    {
+        return _featuresList.size();
+    } //-- int getFeaturesCount() 
+
+    /**
      * Returns the value of field 'id'.
      * 
      * @return int
@@ -157,6 +297,54 @@ public class JSeq implements java.io.Serializable {
     } //-- int getId() 
 
     /**
+     * Method getPdbids
+     * 
+     * 
+     * 
+     * @param index
+     * @return Pdbids
+     */
+    public jalview.binding.Pdbids getPdbids(int index)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _pdbidsList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        
+        return (jalview.binding.Pdbids) _pdbidsList.elementAt(index);
+    } //-- jalview.binding.Pdbids getPdbids(int) 
+
+    /**
+     * Method getPdbids
+     * 
+     * 
+     * 
+     * @return Pdbids
+     */
+    public jalview.binding.Pdbids[] getPdbids()
+    {
+        int size = _pdbidsList.size();
+        jalview.binding.Pdbids[] mArray = new jalview.binding.Pdbids[size];
+        for (int index = 0; index < size; index++) {
+            mArray[index] = (jalview.binding.Pdbids) _pdbidsList.elementAt(index);
+        }
+        return mArray;
+    } //-- jalview.binding.Pdbids[] getPdbids() 
+
+    /**
+     * Method getPdbidsCount
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int getPdbidsCount()
+    {
+        return _pdbidsList.size();
+    } //-- int getPdbidsCount() 
+
+    /**
      * Returns the value of field 'start'.
      * 
      * @return int
@@ -262,6 +450,54 @@ public class JSeq implements java.io.Serializable {
     } //-- void marshal(org.xml.sax.ContentHandler) 
 
     /**
+     * Method removeAllFeatures
+     * 
+     */
+    public void removeAllFeatures()
+    {
+        _featuresList.removeAllElements();
+    } //-- void removeAllFeatures() 
+
+    /**
+     * Method removeAllPdbids
+     * 
+     */
+    public void removeAllPdbids()
+    {
+        _pdbidsList.removeAllElements();
+    } //-- void removeAllPdbids() 
+
+    /**
+     * Method removeFeatures
+     * 
+     * 
+     * 
+     * @param index
+     * @return Features
+     */
+    public jalview.binding.Features removeFeatures(int index)
+    {
+        java.lang.Object obj = _featuresList.elementAt(index);
+        _featuresList.removeElementAt(index);
+        return (jalview.binding.Features) obj;
+    } //-- jalview.binding.Features removeFeatures(int) 
+
+    /**
+     * Method removePdbids
+     * 
+     * 
+     * 
+     * @param index
+     * @return Pdbids
+     */
+    public jalview.binding.Pdbids removePdbids(int index)
+    {
+        java.lang.Object obj = _pdbidsList.elementAt(index);
+        _pdbidsList.removeElementAt(index);
+        return (jalview.binding.Pdbids) obj;
+    } //-- jalview.binding.Pdbids removePdbids(int) 
+
+    /**
      * Sets the value of field 'colour'.
      * 
      * @param colour the value of field 'colour'.
@@ -284,6 +520,40 @@ public class JSeq implements java.io.Serializable {
     } //-- void setEnd(int) 
 
     /**
+     * Method setFeatures
+     * 
+     * 
+     * 
+     * @param index
+     * @param vFeatures
+     */
+    public void setFeatures(int index, jalview.binding.Features vFeatures)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _featuresList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        _featuresList.setElementAt(vFeatures, index);
+    } //-- void setFeatures(int, jalview.binding.Features) 
+
+    /**
+     * Method setFeatures
+     * 
+     * 
+     * 
+     * @param featuresArray
+     */
+    public void setFeatures(jalview.binding.Features[] featuresArray)
+    {
+        //-- copy array
+        _featuresList.removeAllElements();
+        for (int i = 0; i < featuresArray.length; i++) {
+            _featuresList.addElement(featuresArray[i]);
+        }
+    } //-- void setFeatures(jalview.binding.Features) 
+
+    /**
      * Sets the value of field 'id'.
      * 
      * @param id the value of field 'id'.
@@ -295,6 +565,40 @@ public class JSeq implements java.io.Serializable {
     } //-- void setId(int) 
 
     /**
+     * Method setPdbids
+     * 
+     * 
+     * 
+     * @param index
+     * @param vPdbids
+     */
+    public void setPdbids(int index, jalview.binding.Pdbids vPdbids)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _pdbidsList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        _pdbidsList.setElementAt(vPdbids, index);
+    } //-- void setPdbids(int, jalview.binding.Pdbids) 
+
+    /**
+     * Method setPdbids
+     * 
+     * 
+     * 
+     * @param pdbidsArray
+     */
+    public void setPdbids(jalview.binding.Pdbids[] pdbidsArray)
+    {
+        //-- copy array
+        _pdbidsList.removeAllElements();
+        for (int i = 0; i < pdbidsArray.length; i++) {
+            _pdbidsList.addElement(pdbidsArray[i]);
+        }
+    } //-- void setPdbids(jalview.binding.Pdbids) 
+
+    /**
      * Sets the value of field 'start'.
      * 
      * @param start the value of field 'start'.