*/\r
\r
/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-package vamsas.objects.simple;\r
-\r
-public class Alignment extends vamsas.objects.simple.Object\r
- implements java.io.Serializable {\r
- private java.lang.String gapchar;\r
- private java.lang.String[] method;\r
- private vamsas.objects.simple.SequenceSet seqs;\r
- private java.lang.Object __equalsCalc = null;\r
- private boolean __hashCodeCalc = false;\r
-\r
- public Alignment() {\r
- }\r
-\r
- public Alignment(java.lang.String gapchar, java.lang.String[] method,\r
- vamsas.objects.simple.SequenceSet seqs) {\r
- this.gapchar = gapchar;\r
- this.method = method;\r
- this.seqs = seqs;\r
- }\r
-\r
- /**\r
- * Gets the gapchar value for this Alignment.\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
*\r
- * @return gapchar\r
- */\r
- public java.lang.String getGapchar() {\r
- return gapchar;\r
- }\r
-\r
- /**\r
- * Sets the gapchar value for this Alignment.\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
*\r
- * @param gapchar\r
- */\r
- public void setGapchar(java.lang.String gapchar) {\r
- this.gapchar = gapchar;\r
- }\r
-\r
- /**\r
- * Gets the method value for this Alignment.\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
*\r
- * @return method\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
- public java.lang.String[] getMethod() {\r
- return method;\r
- }\r
+package vamsas.objects.simple;\r
\r
- /**\r
- * Sets the method value for this Alignment.\r
- *\r
- * @param method\r
- */\r
- public void setMethod(java.lang.String[] method) {\r
- this.method = method;\r
+public class Alignment\r
+ extends vamsas.objects.simple.Object implements java.io.Serializable\r
+{\r
+ private java.lang.String gapchar;\r
+ private java.lang.String[] method;\r
+ private vamsas.objects.simple.SequenceSet seqs;\r
+ private java.lang.Object __equalsCalc = null;\r
+ private boolean __hashCodeCalc = false;\r
+\r
+ public Alignment()\r
+ {\r
+ }\r
+\r
+ public Alignment(java.lang.String gapchar, java.lang.String[] method,\r
+ vamsas.objects.simple.SequenceSet seqs)\r
+ {\r
+ this.gapchar = gapchar;\r
+ this.method = method;\r
+ this.seqs = seqs;\r
+ }\r
+\r
+ /**\r
+ * Gets the gapchar value for this Alignment.\r
+ *\r
+ * @return gapchar\r
+ */\r
+ public java.lang.String getGapchar()\r
+ {\r
+ return gapchar;\r
+ }\r
+\r
+ /**\r
+ * Sets the gapchar value for this Alignment.\r
+ *\r
+ * @param gapchar\r
+ */\r
+ public void setGapchar(java.lang.String gapchar)\r
+ {\r
+ this.gapchar = gapchar;\r
+ }\r
+\r
+ /**\r
+ * Gets the method value for this Alignment.\r
+ *\r
+ * @return method\r
+ */\r
+ public java.lang.String[] getMethod()\r
+ {\r
+ return method;\r
+ }\r
+\r
+ /**\r
+ * Sets the method value for this Alignment.\r
+ *\r
+ * @param method\r
+ */\r
+ public void setMethod(java.lang.String[] method)\r
+ {\r
+ this.method = method;\r
+ }\r
+\r
+ /**\r
+ * Gets the seqs value for this Alignment.\r
+ *\r
+ * @return seqs\r
+ */\r
+ public vamsas.objects.simple.SequenceSet getSeqs()\r
+ {\r
+ return seqs;\r
+ }\r
+\r
+ /**\r
+ * Sets the seqs value for this Alignment.\r
+ *\r
+ * @param seqs\r
+ */\r
+ public void setSeqs(vamsas.objects.simple.SequenceSet seqs)\r
+ {\r
+ this.seqs = seqs;\r
+ }\r
+\r
+ public synchronized boolean equals(java.lang.Object obj)\r
+ {\r
+ if (! (obj instanceof Alignment))\r
+ {\r
+ return false;\r
}\r
\r
- /**\r
- * Gets the seqs value for this Alignment.\r
- *\r
- * @return seqs\r
- */\r
- public vamsas.objects.simple.SequenceSet getSeqs() {\r
- return seqs;\r
- }\r
+ Alignment other = (Alignment) obj;\r
\r
- /**\r
- * Sets the seqs value for this Alignment.\r
- *\r
- * @param seqs\r
- */\r
- public void setSeqs(vamsas.objects.simple.SequenceSet seqs) {\r
- this.seqs = seqs;\r
+ if (obj == null)\r
+ {\r
+ return false;\r
}\r
\r
- public synchronized boolean equals(java.lang.Object obj) {\r
- if (!(obj instanceof Alignment)) {\r
- return false;\r
- }\r
-\r
- Alignment other = (Alignment) obj;\r
-\r
- if (obj == null) {\r
- return false;\r
- }\r
-\r
- if (this == obj) {\r
- return true;\r
- }\r
-\r
- if (__equalsCalc != null) {\r
- return (__equalsCalc == obj);\r
- }\r
-\r
- __equalsCalc = obj;\r
-\r
- boolean _equals;\r
- _equals = super.equals(obj) &&\r
- (((this.gapchar == null) && (other.getGapchar() == null)) ||\r
- ((this.gapchar != null) && this.gapchar.equals(other.getGapchar()))) &&\r
- (((this.method == null) && (other.getMethod() == null)) ||\r
- ((this.method != null) &&\r
- java.util.Arrays.equals(this.method, other.getMethod()))) &&\r
- (((this.seqs == null) && (other.getSeqs() == null)) ||\r
- ((this.seqs != null) && this.seqs.equals(other.getSeqs())));\r
- __equalsCalc = null;\r
-\r
- return _equals;\r
+ if (this == obj)\r
+ {\r
+ return true;\r
}\r
\r
- public synchronized int hashCode() {\r
- if (__hashCodeCalc) {\r
- return 0;\r
- }\r
+ if (__equalsCalc != null)\r
+ {\r
+ return (__equalsCalc == obj);\r
+ }\r
\r
- __hashCodeCalc = true;\r
+ __equalsCalc = obj;\r
+\r
+ boolean _equals;\r
+ _equals = super.equals(obj) &&\r
+ ( ( (this.gapchar == null) && (other.getGapchar() == null)) ||\r
+ ( (this.gapchar != null) && this.gapchar.equals(other.getGapchar()))) &&\r
+ ( ( (this.method == null) && (other.getMethod() == null)) ||\r
+ ( (this.method != null) &&\r
+ java.util.Arrays.equals(this.method, other.getMethod()))) &&\r
+ ( ( (this.seqs == null) && (other.getSeqs() == null)) ||\r
+ ( (this.seqs != null) && this.seqs.equals(other.getSeqs())));\r
+ __equalsCalc = null;\r
+\r
+ return _equals;\r
+ }\r
+\r
+ public synchronized int hashCode()\r
+ {\r
+ if (__hashCodeCalc)\r
+ {\r
+ return 0;\r
+ }\r
\r
- int _hashCode = super.hashCode();\r
+ __hashCodeCalc = true;\r
\r
- if (getGapchar() != null) {\r
- _hashCode += getGapchar().hashCode();\r
- }\r
+ int _hashCode = super.hashCode();\r
\r
- if (getMethod() != null) {\r
- for (int i = 0; i < java.lang.reflect.Array.getLength(getMethod());\r
- i++) {\r
- java.lang.Object obj = java.lang.reflect.Array.get(getMethod(),\r
- i);\r
+ if (getGapchar() != null)\r
+ {\r
+ _hashCode += getGapchar().hashCode();\r
+ }\r
\r
- if ((obj != null) && !obj.getClass().isArray()) {\r
- _hashCode += obj.hashCode();\r
- }\r
- }\r
+ if (getMethod() != null)\r
+ {\r
+ for (int i = 0; i < java.lang.reflect.Array.getLength(getMethod());\r
+ i++)\r
+ {\r
+ java.lang.Object obj = java.lang.reflect.Array.get(getMethod(),\r
+ i);\r
+\r
+ if ( (obj != null) && !obj.getClass().isArray())\r
+ {\r
+ _hashCode += obj.hashCode();\r
}\r
+ }\r
+ }\r
\r
- if (getSeqs() != null) {\r
- _hashCode += getSeqs().hashCode();\r
- }\r
+ if (getSeqs() != null)\r
+ {\r
+ _hashCode += getSeqs().hashCode();\r
+ }\r
\r
- __hashCodeCalc = false;\r
+ __hashCodeCalc = false;\r
\r
- return _hashCode;\r
- }\r
+ return _hashCode;\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff