X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fuk%2Fac%2Fvamsas%2Fobjects%2Fcore%2FGlyph.java;h=132ff04ff802a929adb7c5ee17cbdc9d94ddbabb;hb=1eea4b639911330e7cd65e17c5421cc584f0d22e;hp=ae9125214fcad66f344fe7c4b8494805bd1dc90a;hpb=ac12127b5cf22bb34b6042e543d506894164a94c;p=vamsas.git
diff --git a/src/uk/ac/vamsas/objects/core/Glyph.java b/src/uk/ac/vamsas/objects/core/Glyph.java
index ae91252..132ff04 100644
--- a/src/uk/ac/vamsas/objects/core/Glyph.java
+++ b/src/uk/ac/vamsas/objects/core/Glyph.java
@@ -1,14 +1,28 @@
/*
- * This class was automatically generated with
- * Castor 1.1, using an XML
- * Schema.
- * $Id$
+ * This file is part of the Vamsas Client version 0.2.
+ * Copyright 2010 by Jim Procter, Iain Milne, Pierre Marguerite,
+ * Andrew Waterhouse and Dominik Lindner.
+ *
+ * Earlier versions have also been incorporated into Jalview version 2.4
+ * since 2008, and TOPALi version 2 since 2007.
+ *
+ * The Vamsas Client 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, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * The Vamsas Client is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with the Vamsas Client. If not, see .
*/
-
package uk.ac.vamsas.objects.core;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
@@ -16,236 +30,271 @@ import org.exolab.castor.xml.Unmarshaller;
/**
* Discrete symbol - possibly graphically represented
- *
+ *
*
* @version $Revision$ $Date$
*/
-public class Glyph extends uk.ac.vamsas.client.Vobject
-implements java.io.Serializable
-{
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * internal content storage
- */
- private java.lang.String _content = "";
-
- /**
- * specifies the symbol dictionary for this
- * glyph - eg utf8 (the default), aasecstr_3 or
- * kd_hydrophobicity - the content is not validated so
- * applications must ensure they gracefully deal with
- * invalid entries here
- */
- private java.lang.String _dict = "utf8";
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Glyph() {
- super();
- setContent("");
- setDict("utf8");
- }
+public class Glyph extends uk.ac.vamsas.client.Vobject implements
+ java.io.Serializable {
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+ /**
+ * internal content storage
+ */
+ private java.lang.String _content = "";
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Overrides the java.lang.Object.equals method.
- *
- * @param obj
- * @return true if the objects are equal.
- */
- public boolean equals(
- final java.lang.Object obj) {
- if ( this == obj )
- return true;
-
- if (super.equals(obj)==false)
+ /**
+ * specifies the symbol dictionary for this glyph - eg utf8 (the default),
+ * aasecstr_3 or kd_hydrophobicity - the content is not validated so
+ * applications must ensure they gracefully deal with invalid entries here
+ */
+ private java.lang.String _dict = "utf8";
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public Glyph() {
+ super();
+ setContent("");
+ setDict("utf8");
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Overrides the java.lang.Object.equals method.
+ *
+ * @param obj
+ * @return true if the objects are equal.
+ */
+ public boolean equals(final java.lang.Object obj) {
+ if (this == obj)
+ return true;
+
+ if (super.equals(obj) == false)
+ return false;
+
+ if (obj instanceof Glyph) {
+
+ Glyph temp = (Glyph) obj;
+ boolean thcycle;
+ boolean tmcycle;
+ if (this._content != null) {
+ if (temp._content == null)
+ return false;
+ if (this._content != temp._content) {
+ thcycle = org.castor.util.CycleBreaker.startingToCycle(this._content);
+ tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._content);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._content);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._content);
+ }
+ ;
return false;
-
- if (obj instanceof Glyph) {
-
- Glyph temp = (Glyph)obj;
- if (this._content != null) {
- if (temp._content == null) return false;
- else if (!(this._content.equals(temp._content)))
- return false;
+ }
+ if (!thcycle) {
+ if (!this._content.equals(temp._content)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._content);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._content);
+ return false;
}
- else if (temp._content != null)
- return false;
- if (this._dict != null) {
- if (temp._dict == null) return false;
- else if (!(this._dict.equals(temp._dict)))
- return false;
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._content);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._content);
+ }
+ }
+ } else if (temp._content != null)
+ return false;
+ if (this._dict != null) {
+ if (temp._dict == null)
+ return false;
+ if (this._dict != temp._dict) {
+ thcycle = org.castor.util.CycleBreaker.startingToCycle(this._dict);
+ tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._dict);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._dict);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._dict);
}
- else if (temp._dict != null)
- return false;
- return true;
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._dict.equals(temp._dict)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._dict);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._dict);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._dict);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._dict);
+ }
}
+ } else if (temp._dict != null)
return false;
+ return true;
}
+ return false;
+ }
- /**
- * Returns the value of field 'content'. The field 'content'
- * has the following description: internal content storage
- *
- * @return the value of field 'Content'.
- */
- public java.lang.String getContent(
- ) {
- return this._content;
- }
+ /**
+ * Returns the value of field 'content'. The field 'content' has the following
+ * description: internal content storage
+ *
+ * @return the value of field 'Content'.
+ */
+ public java.lang.String getContent() {
+ return this._content;
+ }
- /**
- * Returns the value of field 'dict'. The field 'dict' has the
- * following description: specifies the symbol dictionary for
- * this
- * glyph - eg utf8 (the default), aasecstr_3 or
- * kd_hydrophobicity - the content is not validated so
- * applications must ensure they gracefully deal with
- * invalid entries here
- *
- * @return the value of field 'Dict'.
- */
- public java.lang.String getDict(
- ) {
- return this._dict;
- }
+ /**
+ * Returns the value of field 'dict'. The field 'dict' has the following
+ * description: specifies the symbol dictionary for this glyph - eg utf8 (the
+ * default), aasecstr_3 or kd_hydrophobicity - the content is not validated so
+ * applications must ensure they gracefully deal with invalid entries here
+ *
+ * @return the value of field 'Dict'.
+ */
+ public java.lang.String getDict() {
+ return this._dict;
+ }
- /**
- * Overrides the java.lang.Object.hashCode method.
- *
- * The following steps came from Effective Java Programming
- * Language Guide by Joshua Bloch, Chapter 3
- *
- * @return a hash code value for the object.
- */
- public int hashCode(
- ) {
- int result = super.hashCode();
-
- long tmp;
- if (_content != null) {
- result = 37 * result + _content.hashCode();
- }
- if (_dict != null) {
- result = 37 * result + _dict.hashCode();
- }
-
- return result;
- }
+ /**
+ * Overrides the java.lang.Object.hashCode method.
+ *
+ * The following steps came from Effective Java Programming Language
+ * Guide by Joshua Bloch, Chapter 3
+ *
+ * @return a hash code value for the object.
+ */
+ public int hashCode() {
+ int result = super.hashCode();
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
+ long tmp;
+ if (_content != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_content)) {
+ result = 37 * result + _content.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_content);
}
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
+ if (_dict != null && !org.castor.util.CycleBreaker.startingToCycle(_dict)) {
+ result = 37 * result + _dict.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_dict);
}
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
+ return result;
+ }
- /**
- * Sets the value of field 'content'. The field 'content' has
- * the following description: internal content storage
- *
- * @param content the value of field 'content'.
- */
- public void setContent(
- final java.lang.String content) {
- this._content = content;
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid() {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
}
+ return true;
+ }
- /**
- * Sets the value of field 'dict'. The field 'dict' has the
- * following description: specifies the symbol dictionary for
- * this
- * glyph - eg utf8 (the default), aasecstr_3 or
- * kd_hydrophobicity - the content is not validated so
- * applications must ensure they gracefully deal with
- * invalid entries here
- *
- * @param dict the value of field 'dict'.
- */
- public void setDict(
- final java.lang.String dict) {
- this._dict = dict;
- }
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled uk.ac.vamsas.objects.core.Glyph
- */
- public static uk.ac.vamsas.objects.core.Glyph unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (uk.ac.vamsas.objects.core.Glyph) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.Glyph.class, reader);
- }
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+ /**
+ * Sets the value of field 'content'. The field 'content' has the following
+ * description: internal content storage
+ *
+ * @param content
+ * the value of field 'content'.
+ */
+ public void setContent(final java.lang.String content) {
+ this._content = content;
+ }
+
+ /**
+ * Sets the value of field 'dict'. The field 'dict' has the following
+ * description: specifies the symbol dictionary for this glyph - eg utf8 (the
+ * default), aasecstr_3 or kd_hydrophobicity - the content is not validated so
+ * applications must ensure they gracefully deal with invalid entries here
+ *
+ * @param dict
+ * the value of field 'dict'.
+ */
+ public void setDict(final java.lang.String dict) {
+ this._dict = dict;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled uk.ac.vamsas.objects.core.Glyph
+ */
+ public static uk.ac.vamsas.objects.core.Glyph unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException {
+ return (uk.ac.vamsas.objects.core.Glyph) Unmarshaller.unmarshal(
+ uk.ac.vamsas.objects.core.Glyph.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}