+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package MCview;\r
import java.util.*;\r
import java.awt.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package MCview;\r
\r
import java.awt.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package MCview;\r
\r
public class MCMatrix {\r
-/* Copyright (C) 1998 Michele Clamp\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., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.\r
- */\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package MCview;\r
\r
import jalview.datamodel.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package MCview;\r
\r
import jalview.datamodel.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package MCview;\r
\r
import java.util.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package MCview;\r
\r
import java.util.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package MCview;\r
\r
import java.util.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package MCview;\r
// JBPNote TODO: This class is quite noisy - needs proper log.info/log.debug\r
import java.awt.*;\r
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
*/
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+
package ext.vamsas;
public interface JPredWS extends java.rmi.Remote {
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
*/
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+
package ext.vamsas;
public interface JPredWSService extends javax.xml.rpc.Service {
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
*/
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+
package ext.vamsas;
public class JPredWSServiceLocator extends org.apache.axis.client.Service implements ext.vamsas.JPredWSService {
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
*/
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+
package ext.vamsas;
public class JpredResult extends ext.vamsas.Result implements java.io.Serializable {
/**
* Gets the aligfile value for this JpredResult.
- *
+ *
* @return aligfile
*/
public java.lang.String getAligfile() {
/**
* Sets the aligfile value for this JpredResult.
- *
+ *
* @param aligfile
*/
public void setAligfile(java.lang.String aligfile) {
/**
* Gets the predfile value for this JpredResult.
- *
+ *
* @return predfile
*/
public java.lang.String getPredfile() {
/**
* Sets the predfile value for this JpredResult.
- *
+ *
* @param predfile
*/
public void setPredfile(java.lang.String predfile) {
}
__equalsCalc = obj;
boolean _equals;
- _equals = super.equals(obj) &&
- ((this.aligfile==null && other.getAligfile()==null) ||
+ _equals = super.equals(obj) &&
+ ((this.aligfile==null && other.getAligfile()==null) ||
(this.aligfile!=null &&
this.aligfile.equals(other.getAligfile()))) &&
- ((this.predfile==null && other.getPredfile()==null) ||
+ ((this.predfile==null && other.getPredfile()==null) ||
(this.predfile!=null &&
this.predfile.equals(other.getPredfile())));
__equalsCalc = null;
* Get Custom Serializer
*/
public static org.apache.axis.encoding.Serializer getSerializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
+ java.lang.String mechType,
+ java.lang.Class _javaType,
javax.xml.namespace.QName _xmlType) {
- return
+ return
new org.apache.axis.encoding.ser.BeanSerializer(
_javaType, _xmlType, typeDesc);
}
* Get Custom Deserializer
*/
public static org.apache.axis.encoding.Deserializer getDeserializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
+ java.lang.String mechType,
+ java.lang.Class _javaType,
javax.xml.namespace.QName _xmlType) {
- return
+ return
new org.apache.axis.encoding.ser.BeanDeserializer(
_javaType, _xmlType, typeDesc);
}
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
*/
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+
package ext.vamsas;
public class JpredSoapBindingStub extends org.apache.axis.client.Stub implements ext.vamsas.JPredWS {
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
*/
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+
package ext.vamsas;
public class Msfalignment implements java.io.Serializable {
/**
* Gets the msf value for this Msfalignment.
- *
+ *
* @return msf
*/
public java.lang.String getMsf() {
/**
* Sets the msf value for this Msfalignment.
- *
+ *
* @param msf
*/
public void setMsf(java.lang.String msf) {
/**
* Gets the notes value for this Msfalignment.
- *
+ *
* @return notes
*/
public java.lang.String getNotes() {
/**
* Sets the notes value for this Msfalignment.
- *
+ *
* @param notes
*/
public void setNotes(java.lang.String notes) {
}
__equalsCalc = obj;
boolean _equals;
- _equals = true &&
- ((this.msf==null && other.getMsf()==null) ||
+ _equals = true &&
+ ((this.msf==null && other.getMsf()==null) ||
(this.msf!=null &&
this.msf.equals(other.getMsf()))) &&
- ((this.notes==null && other.getNotes()==null) ||
+ ((this.notes==null && other.getNotes()==null) ||
(this.notes!=null &&
this.notes.equals(other.getNotes())));
__equalsCalc = null;
* Get Custom Serializer
*/
public static org.apache.axis.encoding.Serializer getSerializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
+ java.lang.String mechType,
+ java.lang.Class _javaType,
javax.xml.namespace.QName _xmlType) {
- return
+ return
new org.apache.axis.encoding.ser.BeanSerializer(
_javaType, _xmlType, typeDesc);
}
* Get Custom Deserializer
*/
public static org.apache.axis.encoding.Deserializer getDeserializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
+ java.lang.String mechType,
+ java.lang.Class _javaType,
javax.xml.namespace.QName _xmlType) {
- return
+ return
new org.apache.axis.encoding.ser.BeanDeserializer(
_javaType, _xmlType, typeDesc);
}
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
*/
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+
package ext.vamsas;
public interface MuscleWS extends java.rmi.Remote {
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
*/
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+
package ext.vamsas;
public interface MuscleWSService extends javax.xml.rpc.Service {
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
*/
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+
package ext.vamsas;
public class MuscleWSServiceLocator extends org.apache.axis.client.Service implements ext.vamsas.MuscleWSService {
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
*/
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+
package ext.vamsas;
public class MuscleWSSoapBindingStub extends org.apache.axis.client.Stub implements ext.vamsas.MuscleWS {
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
*/
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+
package ext.vamsas;
public class Result implements java.io.Serializable {
/**
* Gets the broken value for this Result.
- *
+ *
* @return broken
*/
public boolean isBroken() {
/**
* Sets the broken value for this Result.
- *
+ *
* @param broken
*/
public void setBroken(boolean broken) {
/**
* Gets the failed value for this Result.
- *
+ *
* @return failed
*/
public boolean isFailed() {
/**
* Sets the failed value for this Result.
- *
+ *
* @param failed
*/
public void setFailed(boolean failed) {
/**
* Gets the finished value for this Result.
- *
+ *
* @return finished
*/
public boolean isFinished() {
/**
* Sets the finished value for this Result.
- *
+ *
* @param finished
*/
public void setFinished(boolean finished) {
/**
* Gets the invalid value for this Result.
- *
+ *
* @return invalid
*/
public boolean isInvalid() {
/**
* Sets the invalid value for this Result.
- *
+ *
* @param invalid
*/
public void setInvalid(boolean invalid) {
/**
* Gets the jobFailed value for this Result.
- *
+ *
* @return jobFailed
*/
public boolean isJobFailed() {
/**
* Sets the jobFailed value for this Result.
- *
+ *
* @param jobFailed
*/
public void setJobFailed(boolean jobFailed) {
/**
* Gets the queued value for this Result.
- *
+ *
* @return queued
*/
public boolean isQueued() {
/**
* Sets the queued value for this Result.
- *
+ *
* @param queued
*/
public void setQueued(boolean queued) {
/**
* Gets the running value for this Result.
- *
+ *
* @return running
*/
public boolean isRunning() {
/**
* Sets the running value for this Result.
- *
+ *
* @param running
*/
public void setRunning(boolean running) {
/**
* Gets the serverError value for this Result.
- *
+ *
* @return serverError
*/
public boolean isServerError() {
/**
* Sets the serverError value for this Result.
- *
+ *
* @param serverError
*/
public void setServerError(boolean serverError) {
/**
* Gets the state value for this Result.
- *
+ *
* @return state
*/
public int getState() {
/**
* Sets the state value for this Result.
- *
+ *
* @param state
*/
public void setState(int state) {
/**
* Gets the status value for this Result.
- *
+ *
* @return status
*/
public java.lang.String getStatus() {
/**
* Sets the status value for this Result.
- *
+ *
* @param status
*/
public void setStatus(java.lang.String status) {
/**
* Gets the suspended value for this Result.
- *
+ *
* @return suspended
*/
public boolean isSuspended() {
/**
* Sets the suspended value for this Result.
- *
+ *
* @param suspended
*/
public void setSuspended(boolean suspended) {
}
__equalsCalc = obj;
boolean _equals;
- _equals = true &&
+ _equals = true &&
this.broken == other.isBroken() &&
this.failed == other.isFailed() &&
this.finished == other.isFinished() &&
this.running == other.isRunning() &&
this.serverError == other.isServerError() &&
this.state == other.getState() &&
- ((this.status==null && other.getStatus()==null) ||
+ ((this.status==null && other.getStatus()==null) ||
(this.status!=null &&
this.status.equals(other.getStatus()))) &&
this.suspended == other.isSuspended();
* Get Custom Serializer
*/
public static org.apache.axis.encoding.Serializer getSerializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
+ java.lang.String mechType,
+ java.lang.Class _javaType,
javax.xml.namespace.QName _xmlType) {
- return
+ return
new org.apache.axis.encoding.ser.BeanSerializer(
_javaType, _xmlType, typeDesc);
}
* Get Custom Deserializer
*/
public static org.apache.axis.encoding.Deserializer getDeserializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
+ java.lang.String mechType,
+ java.lang.Class _javaType,
javax.xml.namespace.QName _xmlType) {
- return
+ return
new org.apache.axis.encoding.ser.BeanDeserializer(
_javaType, _xmlType, typeDesc);
}
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
*/
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+
package ext.vamsas;
public class Secstructpred implements java.io.Serializable {
/**
* Gets the output value for this Secstructpred.
- *
+ *
* @return output
*/
public java.lang.String getOutput() {
/**
* Sets the output value for this Secstructpred.
- *
+ *
* @param output
*/
public void setOutput(java.lang.String output) {
}
__equalsCalc = obj;
boolean _equals;
- _equals = true &&
- ((this.output==null && other.getOutput()==null) ||
+ _equals = true &&
+ ((this.output==null && other.getOutput()==null) ||
(this.output!=null &&
this.output.equals(other.getOutput())));
__equalsCalc = null;
* Get Custom Serializer
*/
public static org.apache.axis.encoding.Serializer getSerializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
+ java.lang.String mechType,
+ java.lang.Class _javaType,
javax.xml.namespace.QName _xmlType) {
- return
+ return
new org.apache.axis.encoding.ser.BeanSerializer(
_javaType, _xmlType, typeDesc);
}
* Get Custom Deserializer
*/
public static org.apache.axis.encoding.Deserializer getDeserializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
+ java.lang.String mechType,
+ java.lang.Class _javaType,
javax.xml.namespace.QName _xmlType) {
- return
+ return
new org.apache.axis.encoding.ser.BeanDeserializer(
_javaType, _xmlType, typeDesc);
}
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
*/
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+
package ext.vamsas;
public class Sequence implements java.io.Serializable {
/**
* Gets the id value for this Sequence.
- *
+ *
* @return id
*/
public java.lang.String getId() {
/**
* Sets the id value for this Sequence.
- *
+ *
* @param id
*/
public void setId(java.lang.String id) {
/**
* Gets the seq value for this Sequence.
- *
+ *
* @return seq
*/
public java.lang.String getSeq() {
/**
* Sets the seq value for this Sequence.
- *
+ *
* @param seq
*/
public void setSeq(java.lang.String seq) {
}
__equalsCalc = obj;
boolean _equals;
- _equals = true &&
- ((this.id==null && other.getId()==null) ||
+ _equals = true &&
+ ((this.id==null && other.getId()==null) ||
(this.id!=null &&
this.id.equals(other.getId()))) &&
- ((this.seq==null && other.getSeq()==null) ||
+ ((this.seq==null && other.getSeq()==null) ||
(this.seq!=null &&
this.seq.equals(other.getSeq())));
__equalsCalc = null;
* Get Custom Serializer
*/
public static org.apache.axis.encoding.Serializer getSerializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
+ java.lang.String mechType,
+ java.lang.Class _javaType,
javax.xml.namespace.QName _xmlType) {
- return
+ return
new org.apache.axis.encoding.ser.BeanSerializer(
_javaType, _xmlType, typeDesc);
}
* Get Custom Deserializer
*/
public static org.apache.axis.encoding.Deserializer getDeserializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
+ java.lang.String mechType,
+ java.lang.Class _javaType,
javax.xml.namespace.QName _xmlType) {
- return
+ return
new org.apache.axis.encoding.ser.BeanDeserializer(
_javaType, _xmlType, typeDesc);
}
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.analysis;\r
\r
import jalview.jbgui.*;\r
-/* Jalview - a java multiple alignment editor\r
- * Copyright (C) 1998 Michele Clamp\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., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.\r
- */\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.analysis;\r
\r
import jalview.schemes.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.analysis;\r
\r
import jalview.datamodel.*;\r
\r
QuickSort.sort(arr,s);\r
\r
- Vector newg = new Vector(nGroup);\r
-\r
- for (int i=nGroup-1; i >= 0; i--) {\r
- newg.addElement(s[i]);\r
- }\r
-\r
- // align.setGroups(newg);\r
+ // align..setGroups(newg);\r
}\r
\r
/**\r
static boolean sortGroupAscending = true;\r
\r
public static void sortByGroup(AlignmentI align) {\r
- int nSeq = align.getHeight();\r
Vector groups = align.getGroups();\r
if (groups.hashCode()!=lastGroupHash) {\r
sortGroupAscending=true;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.analysis;\r
\r
import jalview.datamodel.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.analysis;\r
\r
import jalview.datamodel.*;\r
-/* Jalview - a java multiple alignment editor\r
- * Copyright (C) 1998 Michele Clamp\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., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.\r
- */\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.analysis;\r
\r
\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.analysis;\r
\r
import jalview.datamodel.*;\r
-// PCA.java\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.analysis;\r
\r
import jalview.math.*;\r
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+
package jalview.analysis;
import jalview.datamodel.SequenceI;
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+
package jalview.analysis;
import java.util.Vector;
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.appletgui;\r
\r
import jalview.datamodel.*;\r
-/********************\r
- * 2004 Jalview Reengineered\r
- * Barton Group\r
- * Dundee University\r
- *\r
- * AM Waterhouse\r
- *****************a**/\r
-\r
-\r
-\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
\r
package jalview.appletgui;\r
\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.appletgui;\r
\r
import java.awt.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.appletgui;\r
\r
import jalview.jbappletgui.GAlignmentPanel;\r
\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.appletgui;\r
\r
import java.awt.event.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.appletgui;\r
\r
import jalview.datamodel.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.appletgui;\r
\r
import java.util.*;\r
-/********************\r
- * 2004 Jalview Reengineered\r
- * Barton Group\r
- * Dundee University\r
- *\r
- * AM Waterhouse\r
- *******************/\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
\r
package jalview.appletgui;\r
\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.appletgui;\r
\r
import jalview.datamodel.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.appletgui;\r
\r
import jalview.jbappletgui.GFinder;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.appletgui;\r
\r
import jalview.jbappletgui.GFontChooser;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.appletgui;\r
\r
import java.awt.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.appletgui;\r
\r
import java.awt.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.appletgui;\r
\r
import java.awt.event.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.appletgui;\r
\r
import java.awt.event.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.appletgui;\r
\r
import jalview.datamodel.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.appletgui;\r
import java.awt.*;\r
import java.util.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.appletgui;\r
\r
import jalview.datamodel.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.appletgui;\r
\r
import jalview.jbappletgui.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.appletgui;\r
\r
import jalview.math.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.appletgui;\r
\r
import jalview.datamodel.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.appletgui;\r
\r
import java.awt.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.appletgui;\r
\r
import java.awt.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.appletgui;\r
\r
import jalview.datamodel.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.appletgui;\r
\r
import jalview.jbappletgui.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.appletgui;\r
\r
\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.appletgui;\r
\r
import jalview.datamodel.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.appletgui;\r
\r
import jalview.jbappletgui.GUserDefinedColours;\r
-/********************\r
- * 2004 Jalview Reengineered\r
- * Barton Group\r
- * Dundee University\r
- *\r
- * AM Waterhouse\r
- *******************/\r
-\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
\r
package jalview.bin;\r
import java.util.*;\r
-/********************\r
- * 2004 Jalview Reengineered\r
- * Barton Group\r
- * Dundee University\r
- *\r
- * AM Waterhouse\r
- *******************/\r
-\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
\r
package jalview.bin;\r
\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.bin;\r
\r
import java.applet.*;\r
/*\r
- * This class was automatically generated with \r
+ * This class was automatically generated with\r
* <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.binding;\r
\r
//---------------------------------/\r
\r
/**\r
* Class Alignment.\r
- * \r
+ *\r
* @version $Revision$ $Date$\r
*/\r
public class Alignment implements java.io.Serializable {\r
\r
/**\r
* Returns the value of field 'annotation'.\r
- * \r
+ *\r
* @return Annotation\r
* @return the value of field 'annotation'.\r
*/\r
public jalview.binding.Annotation getAnnotation()\r
{\r
return this._annotation;\r
- } //-- jalview.binding.Annotation getAnnotation() \r
+ } //-- jalview.binding.Annotation getAnnotation()\r
\r
/**\r
* Returns the value of field 'sequenceSet'.\r
- * \r
+ *\r
* @return SequenceSet\r
* @return the value of field 'sequenceSet'.\r
*/\r
public jalview.binding.SequenceSet getSequenceSet()\r
{\r
return this._sequenceSet;\r
- } //-- jalview.binding.SequenceSet getSequenceSet() \r
+ } //-- jalview.binding.SequenceSet getSequenceSet()\r
\r
/**\r
* Method isValid\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean isValid()\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ } //-- boolean isValid()\r
\r
/**\r
* Method marshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param out\r
*/\r
public void marshal(java.io.Writer out)\r
throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- \r
+\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ } //-- void marshal(java.io.Writer)\r
\r
/**\r
* Method marshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param handler\r
*/\r
public void marshal(org.xml.sax.ContentHandler handler)\r
throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- \r
+\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ } //-- void marshal(org.xml.sax.ContentHandler)\r
\r
/**\r
* Sets the value of field 'annotation'.\r
- * \r
+ *\r
* @param annotation the value of field 'annotation'.\r
*/\r
public void setAnnotation(jalview.binding.Annotation annotation)\r
{\r
this._annotation = annotation;\r
- } //-- void setAnnotation(jalview.binding.Annotation) \r
+ } //-- void setAnnotation(jalview.binding.Annotation)\r
\r
/**\r
* Sets the value of field 'sequenceSet'.\r
- * \r
+ *\r
* @param sequenceSet the value of field 'sequenceSet'.\r
*/\r
public void setSequenceSet(jalview.binding.SequenceSet sequenceSet)\r
{\r
this._sequenceSet = sequenceSet;\r
- } //-- void setSequenceSet(jalview.binding.SequenceSet) \r
+ } //-- void setSequenceSet(jalview.binding.SequenceSet)\r
\r
/**\r
* Method unmarshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param reader\r
* @return Object\r
*/\r
throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
return (jalview.binding.Alignment) Unmarshaller.unmarshal(jalview.binding.Alignment.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ } //-- java.lang.Object unmarshal(java.io.Reader)\r
\r
/**\r
* Method validate\r
- * \r
+ *\r
*/\r
public void validate()\r
throws org.exolab.castor.xml.ValidationException\r
{\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ } //-- void validate()\r
\r
}\r
/*\r
- * This class was automatically generated with \r
+ * This class was automatically generated with\r
* <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.binding;\r
\r
//---------------------------------/\r
\r
/**\r
* Class Annotation.\r
- * \r
+ *\r
* @version $Revision$ $Date$\r
*/\r
public class Annotation implements java.io.Serializable {\r
\r
/**\r
* Method addAnnotationElement\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param vAnnotationElement\r
*/\r
public void addAnnotationElement(jalview.binding.AnnotationElement vAnnotationElement)\r
throws java.lang.IndexOutOfBoundsException\r
{\r
_annotationElementList.addElement(vAnnotationElement);\r
- } //-- void addAnnotationElement(jalview.binding.AnnotationElement) \r
+ } //-- void addAnnotationElement(jalview.binding.AnnotationElement)\r
\r
/**\r
* Method addAnnotationElement\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @param vAnnotationElement\r
*/\r
throws java.lang.IndexOutOfBoundsException\r
{\r
_annotationElementList.insertElementAt(vAnnotationElement, index);\r
- } //-- void addAnnotationElement(int, jalview.binding.AnnotationElement) \r
+ } //-- void addAnnotationElement(int, jalview.binding.AnnotationElement)\r
\r
/**\r
* Method deleteGraph\r
- * \r
+ *\r
*/\r
public void deleteGraph()\r
{\r
this._has_graph= false;\r
- } //-- void deleteGraph() \r
+ } //-- void deleteGraph()\r
\r
/**\r
* Method enumerateAnnotationElement\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return Enumeration\r
*/\r
public java.util.Enumeration enumerateAnnotationElement()\r
{\r
return _annotationElementList.elements();\r
- } //-- java.util.Enumeration enumerateAnnotationElement() \r
+ } //-- java.util.Enumeration enumerateAnnotationElement()\r
\r
/**\r
* Method getAnnotationElement\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @return AnnotationElement\r
*/\r
if ((index < 0) || (index > _annotationElementList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
- \r
+\r
return (jalview.binding.AnnotationElement) _annotationElementList.elementAt(index);\r
- } //-- jalview.binding.AnnotationElement getAnnotationElement(int) \r
+ } //-- jalview.binding.AnnotationElement getAnnotationElement(int)\r
\r
/**\r
* Method getAnnotationElement\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return AnnotationElement\r
*/\r
public jalview.binding.AnnotationElement[] getAnnotationElement()\r
mArray[index] = (jalview.binding.AnnotationElement) _annotationElementList.elementAt(index);\r
}\r
return mArray;\r
- } //-- jalview.binding.AnnotationElement[] getAnnotationElement() \r
+ } //-- jalview.binding.AnnotationElement[] getAnnotationElement()\r
\r
/**\r
* Method getAnnotationElementCount\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return int\r
*/\r
public int getAnnotationElementCount()\r
{\r
return _annotationElementList.size();\r
- } //-- int getAnnotationElementCount() \r
+ } //-- int getAnnotationElementCount()\r
\r
/**\r
* Returns the value of field 'description'.\r
- * \r
+ *\r
* @return String\r
* @return the value of field 'description'.\r
*/\r
public java.lang.String getDescription()\r
{\r
return this._description;\r
- } //-- java.lang.String getDescription() \r
+ } //-- java.lang.String getDescription()\r
\r
/**\r
* Returns the value of field 'graph'.\r
- * \r
+ *\r
* @return boolean\r
* @return the value of field 'graph'.\r
*/\r
public boolean getGraph()\r
{\r
return this._graph;\r
- } //-- boolean getGraph() \r
+ } //-- boolean getGraph()\r
\r
/**\r
* Returns the value of field 'label'.\r
- * \r
+ *\r
* @return String\r
* @return the value of field 'label'.\r
*/\r
public java.lang.String getLabel()\r
{\r
return this._label;\r
- } //-- java.lang.String getLabel() \r
+ } //-- java.lang.String getLabel()\r
\r
/**\r
* Method hasGraph\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasGraph()\r
{\r
return this._has_graph;\r
- } //-- boolean hasGraph() \r
+ } //-- boolean hasGraph()\r
\r
/**\r
* Method isValid\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean isValid()\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ } //-- boolean isValid()\r
\r
/**\r
* Method marshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param out\r
*/\r
public void marshal(java.io.Writer out)\r
throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- \r
+\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ } //-- void marshal(java.io.Writer)\r
\r
/**\r
* Method marshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param handler\r
*/\r
public void marshal(org.xml.sax.ContentHandler handler)\r
throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- \r
+\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ } //-- void marshal(org.xml.sax.ContentHandler)\r
\r
/**\r
* Method removeAllAnnotationElement\r
- * \r
+ *\r
*/\r
public void removeAllAnnotationElement()\r
{\r
_annotationElementList.removeAllElements();\r
- } //-- void removeAllAnnotationElement() \r
+ } //-- void removeAllAnnotationElement()\r
\r
/**\r
* Method removeAnnotationElement\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @return AnnotationElement\r
*/\r
java.lang.Object obj = _annotationElementList.elementAt(index);\r
_annotationElementList.removeElementAt(index);\r
return (jalview.binding.AnnotationElement) obj;\r
- } //-- jalview.binding.AnnotationElement removeAnnotationElement(int) \r
+ } //-- jalview.binding.AnnotationElement removeAnnotationElement(int)\r
\r
/**\r
* Method setAnnotationElement\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @param vAnnotationElement\r
*/\r
throw new IndexOutOfBoundsException();\r
}\r
_annotationElementList.setElementAt(vAnnotationElement, index);\r
- } //-- void setAnnotationElement(int, jalview.binding.AnnotationElement) \r
+ } //-- void setAnnotationElement(int, jalview.binding.AnnotationElement)\r
\r
/**\r
* Method setAnnotationElement\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param annotationElementArray\r
*/\r
public void setAnnotationElement(jalview.binding.AnnotationElement[] annotationElementArray)\r
for (int i = 0; i < annotationElementArray.length; i++) {\r
_annotationElementList.addElement(annotationElementArray[i]);\r
}\r
- } //-- void setAnnotationElement(jalview.binding.AnnotationElement) \r
+ } //-- void setAnnotationElement(jalview.binding.AnnotationElement)\r
\r
/**\r
* Sets the value of field 'description'.\r
- * \r
+ *\r
* @param description the value of field 'description'.\r
*/\r
public void setDescription(java.lang.String description)\r
{\r
this._description = description;\r
- } //-- void setDescription(java.lang.String) \r
+ } //-- void setDescription(java.lang.String)\r
\r
/**\r
* Sets the value of field 'graph'.\r
- * \r
+ *\r
* @param graph the value of field 'graph'.\r
*/\r
public void setGraph(boolean graph)\r
{\r
this._graph = graph;\r
this._has_graph = true;\r
- } //-- void setGraph(boolean) \r
+ } //-- void setGraph(boolean)\r
\r
/**\r
* Sets the value of field 'label'.\r
- * \r
+ *\r
* @param label the value of field 'label'.\r
*/\r
public void setLabel(java.lang.String label)\r
{\r
this._label = label;\r
- } //-- void setLabel(java.lang.String) \r
+ } //-- void setLabel(java.lang.String)\r
\r
/**\r
* Method unmarshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param reader\r
* @return Object\r
*/\r
throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
return (jalview.binding.Annotation) Unmarshaller.unmarshal(jalview.binding.Annotation.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ } //-- java.lang.Object unmarshal(java.io.Reader)\r
\r
/**\r
* Method validate\r
- * \r
+ *\r
*/\r
public void validate()\r
throws org.exolab.castor.xml.ValidationException\r
{\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ } //-- void validate()\r
\r
}\r
/*\r
- * This class was automatically generated with \r
+ * This class was automatically generated with\r
* <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.binding;\r
\r
//---------------------------------/\r
\r
/**\r
* Class AnnotationElement.\r
- * \r
+ *\r
* @version $Revision$ $Date$\r
*/\r
public class AnnotationElement implements java.io.Serializable {\r
\r
/**\r
* Method deletePosition\r
- * \r
+ *\r
*/\r
public void deletePosition()\r
{\r
this._has_position= false;\r
- } //-- void deletePosition() \r
+ } //-- void deletePosition()\r
\r
/**\r
* Method deleteValue\r
- * \r
+ *\r
*/\r
public void deleteValue()\r
{\r
this._has_value= false;\r
- } //-- void deleteValue() \r
+ } //-- void deleteValue()\r
\r
/**\r
* Returns the value of field 'description'.\r
- * \r
+ *\r
* @return String\r
* @return the value of field 'description'.\r
*/\r
public java.lang.String getDescription()\r
{\r
return this._description;\r
- } //-- java.lang.String getDescription() \r
+ } //-- java.lang.String getDescription()\r
\r
/**\r
* Returns the value of field 'displayCharacter'.\r
- * \r
+ *\r
* @return String\r
* @return the value of field 'displayCharacter'.\r
*/\r
public java.lang.String getDisplayCharacter()\r
{\r
return this._displayCharacter;\r
- } //-- java.lang.String getDisplayCharacter() \r
+ } //-- java.lang.String getDisplayCharacter()\r
\r
/**\r
* Returns the value of field 'position'.\r
- * \r
+ *\r
* @return int\r
* @return the value of field 'position'.\r
*/\r
public int getPosition()\r
{\r
return this._position;\r
- } //-- int getPosition() \r
+ } //-- int getPosition()\r
\r
/**\r
* Returns the value of field 'secondaryStructure'.\r
- * \r
+ *\r
* @return String\r
* @return the value of field 'secondaryStructure'.\r
*/\r
public java.lang.String getSecondaryStructure()\r
{\r
return this._secondaryStructure;\r
- } //-- java.lang.String getSecondaryStructure() \r
+ } //-- java.lang.String getSecondaryStructure()\r
\r
/**\r
* Returns the value of field 'value'.\r
- * \r
+ *\r
* @return float\r
* @return the value of field 'value'.\r
*/\r
public float getValue()\r
{\r
return this._value;\r
- } //-- float getValue() \r
+ } //-- float getValue()\r
\r
/**\r
* Method hasPosition\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasPosition()\r
{\r
return this._has_position;\r
- } //-- boolean hasPosition() \r
+ } //-- boolean hasPosition()\r
\r
/**\r
* Method hasValue\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasValue()\r
{\r
return this._has_value;\r
- } //-- boolean hasValue() \r
+ } //-- boolean hasValue()\r
\r
/**\r
* Method isValid\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean isValid()\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ } //-- boolean isValid()\r
\r
/**\r
* Method marshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param out\r
*/\r
public void marshal(java.io.Writer out)\r
throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- \r
+\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ } //-- void marshal(java.io.Writer)\r
\r
/**\r
* Method marshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param handler\r
*/\r
public void marshal(org.xml.sax.ContentHandler handler)\r
throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- \r
+\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ } //-- void marshal(org.xml.sax.ContentHandler)\r
\r
/**\r
* Sets the value of field 'description'.\r
- * \r
+ *\r
* @param description the value of field 'description'.\r
*/\r
public void setDescription(java.lang.String description)\r
{\r
this._description = description;\r
- } //-- void setDescription(java.lang.String) \r
+ } //-- void setDescription(java.lang.String)\r
\r
/**\r
* Sets the value of field 'displayCharacter'.\r
- * \r
+ *\r
* @param displayCharacter the value of field 'displayCharacter'\r
*/\r
public void setDisplayCharacter(java.lang.String displayCharacter)\r
{\r
this._displayCharacter = displayCharacter;\r
- } //-- void setDisplayCharacter(java.lang.String) \r
+ } //-- void setDisplayCharacter(java.lang.String)\r
\r
/**\r
* Sets the value of field 'position'.\r
- * \r
+ *\r
* @param position the value of field 'position'.\r
*/\r
public void setPosition(int position)\r
{\r
this._position = position;\r
this._has_position = true;\r
- } //-- void setPosition(int) \r
+ } //-- void setPosition(int)\r
\r
/**\r
* Sets the value of field 'secondaryStructure'.\r
- * \r
+ *\r
* @param secondaryStructure the value of field\r
* 'secondaryStructure'.\r
*/\r
public void setSecondaryStructure(java.lang.String secondaryStructure)\r
{\r
this._secondaryStructure = secondaryStructure;\r
- } //-- void setSecondaryStructure(java.lang.String) \r
+ } //-- void setSecondaryStructure(java.lang.String)\r
\r
/**\r
* Sets the value of field 'value'.\r
- * \r
+ *\r
* @param value the value of field 'value'.\r
*/\r
public void setValue(float value)\r
{\r
this._value = value;\r
this._has_value = true;\r
- } //-- void setValue(float) \r
+ } //-- void setValue(float)\r
\r
/**\r
* Method unmarshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param reader\r
* @return Object\r
*/\r
throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
return (jalview.binding.AnnotationElement) Unmarshaller.unmarshal(jalview.binding.AnnotationElement.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ } //-- java.lang.Object unmarshal(java.io.Reader)\r
\r
/**\r
* Method validate\r
- * \r
+ *\r
*/\r
public void validate()\r
throws org.exolab.castor.xml.ValidationException\r
{\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ } //-- void validate()\r
\r
}\r
/*\r
- * This class was automatically generated with \r
+ * This class was automatically generated with\r
* <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.binding;\r
\r
//---------------------------------/\r
\r
/**\r
* Class Colour.\r
- * \r
+ *\r
* @version $Revision$ $Date$\r
*/\r
public class Colour implements java.io.Serializable {\r
\r
/**\r
* Returns the value of field 'name'.\r
- * \r
+ *\r
* @return String\r
* @return the value of field 'name'.\r
*/\r
public java.lang.String getName()\r
{\r
return this._name;\r
- } //-- java.lang.String getName() \r
+ } //-- java.lang.String getName()\r
\r
/**\r
* Returns the value of field 'RGB'.\r
- * \r
+ *\r
* @return String\r
* @return the value of field 'RGB'.\r
*/\r
public java.lang.String getRGB()\r
{\r
return this._RGB;\r
- } //-- java.lang.String getRGB() \r
+ } //-- java.lang.String getRGB()\r
\r
/**\r
* Method isValid\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean isValid()\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ } //-- boolean isValid()\r
\r
/**\r
* Method marshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param out\r
*/\r
public void marshal(java.io.Writer out)\r
throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- \r
+\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ } //-- void marshal(java.io.Writer)\r
\r
/**\r
* Method marshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param handler\r
*/\r
public void marshal(org.xml.sax.ContentHandler handler)\r
throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- \r
+\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ } //-- void marshal(org.xml.sax.ContentHandler)\r
\r
/**\r
* Sets the value of field 'name'.\r
- * \r
+ *\r
* @param name the value of field 'name'.\r
*/\r
public void setName(java.lang.String name)\r
{\r
this._name = name;\r
- } //-- void setName(java.lang.String) \r
+ } //-- void setName(java.lang.String)\r
\r
/**\r
* Sets the value of field 'RGB'.\r
- * \r
+ *\r
* @param RGB the value of field 'RGB'.\r
*/\r
public void setRGB(java.lang.String RGB)\r
{\r
this._RGB = RGB;\r
- } //-- void setRGB(java.lang.String) \r
+ } //-- void setRGB(java.lang.String)\r
\r
/**\r
* Method unmarshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param reader\r
* @return Object\r
*/\r
throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
return (jalview.binding.Colour) Unmarshaller.unmarshal(jalview.binding.Colour.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ } //-- java.lang.Object unmarshal(java.io.Reader)\r
\r
/**\r
* Method validate\r
- * \r
+ *\r
*/\r
public void validate()\r
throws org.exolab.castor.xml.ValidationException\r
{\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ } //-- void validate()\r
\r
}\r
/*\r
- * This class was automatically generated with \r
+ * This class was automatically generated with\r
* <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.binding;\r
\r
//---------------------------------/\r
\r
/**\r
* Class JGroup.\r
- * \r
+ *\r
* @version $Revision$ $Date$\r
*/\r
public class JGroup implements java.io.Serializable {\r
\r
/**\r
* Method addSeq\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param vSeq\r
*/\r
public void addSeq(int vSeq)\r
throws java.lang.IndexOutOfBoundsException\r
{\r
_seqList.addElement(new java.lang.Integer(vSeq));\r
- } //-- void addSeq(int) \r
+ } //-- void addSeq(int)\r
\r
/**\r
* Method addSeq\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @param vSeq\r
*/\r
throws java.lang.IndexOutOfBoundsException\r
{\r
_seqList.insertElementAt(new java.lang.Integer(vSeq), index);\r
- } //-- void addSeq(int, int) \r
+ } //-- void addSeq(int, int)\r
\r
/**\r
* Method deleteColourText\r
- * \r
+ *\r
*/\r
public void deleteColourText()\r
{\r
this._has_colourText= false;\r
- } //-- void deleteColourText() \r
+ } //-- void deleteColourText()\r
\r
/**\r
* Method deleteConsThreshold\r
- * \r
+ *\r
*/\r
public void deleteConsThreshold()\r
{\r
this._has_consThreshold= false;\r
- } //-- void deleteConsThreshold() \r
+ } //-- void deleteConsThreshold()\r
\r
/**\r
* Method deleteDisplayBoxes\r
- * \r
+ *\r
*/\r
public void deleteDisplayBoxes()\r
{\r
this._has_displayBoxes= false;\r
- } //-- void deleteDisplayBoxes() \r
+ } //-- void deleteDisplayBoxes()\r
\r
/**\r
* Method deleteDisplayText\r
- * \r
+ *\r
*/\r
public void deleteDisplayText()\r
{\r
this._has_displayText= false;\r
- } //-- void deleteDisplayText() \r
+ } //-- void deleteDisplayText()\r
\r
/**\r
* Method deleteEnd\r
- * \r
+ *\r
*/\r
public void deleteEnd()\r
{\r
this._has_end= false;\r
- } //-- void deleteEnd() \r
+ } //-- void deleteEnd()\r
\r
/**\r
* Method deleteOutlineColour\r
- * \r
+ *\r
*/\r
public void deleteOutlineColour()\r
{\r
this._has_outlineColour= false;\r
- } //-- void deleteOutlineColour() \r
+ } //-- void deleteOutlineColour()\r
\r
/**\r
* Method deletePidThreshold\r
- * \r
+ *\r
*/\r
public void deletePidThreshold()\r
{\r
this._has_pidThreshold= false;\r
- } //-- void deletePidThreshold() \r
+ } //-- void deletePidThreshold()\r
\r
/**\r
* Method deleteStart\r
- * \r
+ *\r
*/\r
public void deleteStart()\r
{\r
this._has_start= false;\r
- } //-- void deleteStart() \r
+ } //-- void deleteStart()\r
\r
/**\r
* Method enumerateSeq\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return Enumeration\r
*/\r
public java.util.Enumeration enumerateSeq()\r
{\r
return _seqList.elements();\r
- } //-- java.util.Enumeration enumerateSeq() \r
+ } //-- java.util.Enumeration enumerateSeq()\r
\r
/**\r
* Returns the value of field 'colour'.\r
- * \r
+ *\r
* @return String\r
* @return the value of field 'colour'.\r
*/\r
public java.lang.String getColour()\r
{\r
return this._colour;\r
- } //-- java.lang.String getColour() \r
+ } //-- java.lang.String getColour()\r
\r
/**\r
* Returns the value of field 'colourText'.\r
- * \r
+ *\r
* @return boolean\r
* @return the value of field 'colourText'.\r
*/\r
public boolean getColourText()\r
{\r
return this._colourText;\r
- } //-- boolean getColourText() \r
+ } //-- boolean getColourText()\r
\r
/**\r
* Returns the value of field 'consThreshold'.\r
- * \r
+ *\r
* @return int\r
* @return the value of field 'consThreshold'.\r
*/\r
public int getConsThreshold()\r
{\r
return this._consThreshold;\r
- } //-- int getConsThreshold() \r
+ } //-- int getConsThreshold()\r
\r
/**\r
* Returns the value of field 'displayBoxes'.\r
- * \r
+ *\r
* @return boolean\r
* @return the value of field 'displayBoxes'.\r
*/\r
public boolean getDisplayBoxes()\r
{\r
return this._displayBoxes;\r
- } //-- boolean getDisplayBoxes() \r
+ } //-- boolean getDisplayBoxes()\r
\r
/**\r
* Returns the value of field 'displayText'.\r
- * \r
+ *\r
* @return boolean\r
* @return the value of field 'displayText'.\r
*/\r
public boolean getDisplayText()\r
{\r
return this._displayText;\r
- } //-- boolean getDisplayText() \r
+ } //-- boolean getDisplayText()\r
\r
/**\r
* Returns the value of field 'end'.\r
- * \r
+ *\r
* @return int\r
* @return the value of field 'end'.\r
*/\r
public int getEnd()\r
{\r
return this._end;\r
- } //-- int getEnd() \r
+ } //-- int getEnd()\r
\r
/**\r
* Returns the value of field 'name'.\r
- * \r
+ *\r
* @return String\r
* @return the value of field 'name'.\r
*/\r
public java.lang.String getName()\r
{\r
return this._name;\r
- } //-- java.lang.String getName() \r
+ } //-- java.lang.String getName()\r
\r
/**\r
* Returns the value of field 'outlineColour'.\r
- * \r
+ *\r
* @return int\r
* @return the value of field 'outlineColour'.\r
*/\r
public int getOutlineColour()\r
{\r
return this._outlineColour;\r
- } //-- int getOutlineColour() \r
+ } //-- int getOutlineColour()\r
\r
/**\r
* Returns the value of field 'pidThreshold'.\r
- * \r
+ *\r
* @return int\r
* @return the value of field 'pidThreshold'.\r
*/\r
public int getPidThreshold()\r
{\r
return this._pidThreshold;\r
- } //-- int getPidThreshold() \r
+ } //-- int getPidThreshold()\r
\r
/**\r
* Method getSeq\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @return int\r
*/\r
if ((index < 0) || (index > _seqList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
- \r
+\r
return ((java.lang.Integer)_seqList.elementAt(index)).intValue();\r
- } //-- int getSeq(int) \r
+ } //-- int getSeq(int)\r
\r
/**\r
* Method getSeq\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return int\r
*/\r
public int[] getSeq()\r
mArray[index] = ((java.lang.Integer)_seqList.elementAt(index)).intValue();\r
}\r
return mArray;\r
- } //-- int[] getSeq() \r
+ } //-- int[] getSeq()\r
\r
/**\r
* Method getSeqCount\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return int\r
*/\r
public int getSeqCount()\r
{\r
return _seqList.size();\r
- } //-- int getSeqCount() \r
+ } //-- int getSeqCount()\r
\r
/**\r
* Returns the value of field 'start'.\r
- * \r
+ *\r
* @return int\r
* @return the value of field 'start'.\r
*/\r
public int getStart()\r
{\r
return this._start;\r
- } //-- int getStart() \r
+ } //-- int getStart()\r
\r
/**\r
* Method hasColourText\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasColourText()\r
{\r
return this._has_colourText;\r
- } //-- boolean hasColourText() \r
+ } //-- boolean hasColourText()\r
\r
/**\r
* Method hasConsThreshold\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasConsThreshold()\r
{\r
return this._has_consThreshold;\r
- } //-- boolean hasConsThreshold() \r
+ } //-- boolean hasConsThreshold()\r
\r
/**\r
* Method hasDisplayBoxes\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasDisplayBoxes()\r
{\r
return this._has_displayBoxes;\r
- } //-- boolean hasDisplayBoxes() \r
+ } //-- boolean hasDisplayBoxes()\r
\r
/**\r
* Method hasDisplayText\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasDisplayText()\r
{\r
return this._has_displayText;\r
- } //-- boolean hasDisplayText() \r
+ } //-- boolean hasDisplayText()\r
\r
/**\r
* Method hasEnd\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasEnd()\r
{\r
return this._has_end;\r
- } //-- boolean hasEnd() \r
+ } //-- boolean hasEnd()\r
\r
/**\r
* Method hasOutlineColour\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasOutlineColour()\r
{\r
return this._has_outlineColour;\r
- } //-- boolean hasOutlineColour() \r
+ } //-- boolean hasOutlineColour()\r
\r
/**\r
* Method hasPidThreshold\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasPidThreshold()\r
{\r
return this._has_pidThreshold;\r
- } //-- boolean hasPidThreshold() \r
+ } //-- boolean hasPidThreshold()\r
\r
/**\r
* Method hasStart\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasStart()\r
{\r
return this._has_start;\r
- } //-- boolean hasStart() \r
+ } //-- boolean hasStart()\r
\r
/**\r
* Method isValid\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean isValid()\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ } //-- boolean isValid()\r
\r
/**\r
* Method marshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param out\r
*/\r
public void marshal(java.io.Writer out)\r
throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- \r
+\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ } //-- void marshal(java.io.Writer)\r
\r
/**\r
* Method marshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param handler\r
*/\r
public void marshal(org.xml.sax.ContentHandler handler)\r
throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- \r
+\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ } //-- void marshal(org.xml.sax.ContentHandler)\r
\r
/**\r
* Method removeAllSeq\r
- * \r
+ *\r
*/\r
public void removeAllSeq()\r
{\r
_seqList.removeAllElements();\r
- } //-- void removeAllSeq() \r
+ } //-- void removeAllSeq()\r
\r
/**\r
* Method removeSeq\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @return int\r
*/\r
java.lang.Object obj = _seqList.elementAt(index);\r
_seqList.removeElementAt(index);\r
return ((java.lang.Integer)obj).intValue();\r
- } //-- int removeSeq(int) \r
+ } //-- int removeSeq(int)\r
\r
/**\r
* Sets the value of field 'colour'.\r
- * \r
+ *\r
* @param colour the value of field 'colour'.\r
*/\r
public void setColour(java.lang.String colour)\r
{\r
this._colour = colour;\r
- } //-- void setColour(java.lang.String) \r
+ } //-- void setColour(java.lang.String)\r
\r
/**\r
* Sets the value of field 'colourText'.\r
- * \r
+ *\r
* @param colourText the value of field 'colourText'.\r
*/\r
public void setColourText(boolean colourText)\r
{\r
this._colourText = colourText;\r
this._has_colourText = true;\r
- } //-- void setColourText(boolean) \r
+ } //-- void setColourText(boolean)\r
\r
/**\r
* Sets the value of field 'consThreshold'.\r
- * \r
+ *\r
* @param consThreshold the value of field 'consThreshold'.\r
*/\r
public void setConsThreshold(int consThreshold)\r
{\r
this._consThreshold = consThreshold;\r
this._has_consThreshold = true;\r
- } //-- void setConsThreshold(int) \r
+ } //-- void setConsThreshold(int)\r
\r
/**\r
* Sets the value of field 'displayBoxes'.\r
- * \r
+ *\r
* @param displayBoxes the value of field 'displayBoxes'.\r
*/\r
public void setDisplayBoxes(boolean displayBoxes)\r
{\r
this._displayBoxes = displayBoxes;\r
this._has_displayBoxes = true;\r
- } //-- void setDisplayBoxes(boolean) \r
+ } //-- void setDisplayBoxes(boolean)\r
\r
/**\r
* Sets the value of field 'displayText'.\r
- * \r
+ *\r
* @param displayText the value of field 'displayText'.\r
*/\r
public void setDisplayText(boolean displayText)\r
{\r
this._displayText = displayText;\r
this._has_displayText = true;\r
- } //-- void setDisplayText(boolean) \r
+ } //-- void setDisplayText(boolean)\r
\r
/**\r
* Sets the value of field 'end'.\r
- * \r
+ *\r
* @param end the value of field 'end'.\r
*/\r
public void setEnd(int end)\r
{\r
this._end = end;\r
this._has_end = true;\r
- } //-- void setEnd(int) \r
+ } //-- void setEnd(int)\r
\r
/**\r
* Sets the value of field 'name'.\r
- * \r
+ *\r
* @param name the value of field 'name'.\r
*/\r
public void setName(java.lang.String name)\r
{\r
this._name = name;\r
- } //-- void setName(java.lang.String) \r
+ } //-- void setName(java.lang.String)\r
\r
/**\r
* Sets the value of field 'outlineColour'.\r
- * \r
+ *\r
* @param outlineColour the value of field 'outlineColour'.\r
*/\r
public void setOutlineColour(int outlineColour)\r
{\r
this._outlineColour = outlineColour;\r
this._has_outlineColour = true;\r
- } //-- void setOutlineColour(int) \r
+ } //-- void setOutlineColour(int)\r
\r
/**\r
* Sets the value of field 'pidThreshold'.\r
- * \r
+ *\r
* @param pidThreshold the value of field 'pidThreshold'.\r
*/\r
public void setPidThreshold(int pidThreshold)\r
{\r
this._pidThreshold = pidThreshold;\r
this._has_pidThreshold = true;\r
- } //-- void setPidThreshold(int) \r
+ } //-- void setPidThreshold(int)\r
\r
/**\r
* Method setSeq\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @param vSeq\r
*/\r
throw new IndexOutOfBoundsException();\r
}\r
_seqList.setElementAt(new java.lang.Integer(vSeq), index);\r
- } //-- void setSeq(int, int) \r
+ } //-- void setSeq(int, int)\r
\r
/**\r
* Method setSeq\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param seqArray\r
*/\r
public void setSeq(int[] seqArray)\r
for (int i = 0; i < seqArray.length; i++) {\r
_seqList.addElement(new java.lang.Integer(seqArray[i]));\r
}\r
- } //-- void setSeq(int) \r
+ } //-- void setSeq(int)\r
\r
/**\r
* Sets the value of field 'start'.\r
- * \r
+ *\r
* @param start the value of field 'start'.\r
*/\r
public void setStart(int start)\r
{\r
this._start = start;\r
this._has_start = true;\r
- } //-- void setStart(int) \r
+ } //-- void setStart(int)\r
\r
/**\r
* Method unmarshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param reader\r
* @return Object\r
*/\r
throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
return (jalview.binding.JGroup) Unmarshaller.unmarshal(jalview.binding.JGroup.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ } //-- java.lang.Object unmarshal(java.io.Reader)\r
\r
/**\r
* Method validate\r
- * \r
+ *\r
*/\r
public void validate()\r
throws org.exolab.castor.xml.ValidationException\r
{\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ } //-- void validate()\r
\r
}\r
/*\r
- * This class was automatically generated with \r
+ * This class was automatically generated with\r
* <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.binding;\r
\r
//---------------------------------/\r
\r
/**\r
* Class JSeq.\r
- * \r
+ *\r
* @version $Revision$ $Date$\r
*/\r
public class JSeq implements java.io.Serializable {\r
\r
/**\r
* Method deleteColour\r
- * \r
+ *\r
*/\r
public void deleteColour()\r
{\r
this._has_colour= false;\r
- } //-- void deleteColour() \r
+ } //-- void deleteColour()\r
\r
/**\r
* Method deleteEnd\r
- * \r
+ *\r
*/\r
public void deleteEnd()\r
{\r
this._has_end= false;\r
- } //-- void deleteEnd() \r
+ } //-- void deleteEnd()\r
\r
/**\r
* Method deleteId\r
- * \r
+ *\r
*/\r
public void deleteId()\r
{\r
this._has_id= false;\r
- } //-- void deleteId() \r
+ } //-- void deleteId()\r
\r
/**\r
* Method deleteStart\r
- * \r
+ *\r
*/\r
public void deleteStart()\r
{\r
this._has_start= false;\r
- } //-- void deleteStart() \r
+ } //-- void deleteStart()\r
\r
/**\r
* Returns the value of field 'colour'.\r
- * \r
+ *\r
* @return int\r
* @return the value of field 'colour'.\r
*/\r
public int getColour()\r
{\r
return this._colour;\r
- } //-- int getColour() \r
+ } //-- int getColour()\r
\r
/**\r
* Returns the value of field 'end'.\r
- * \r
+ *\r
* @return int\r
* @return the value of field 'end'.\r
*/\r
public int getEnd()\r
{\r
return this._end;\r
- } //-- int getEnd() \r
+ } //-- int getEnd()\r
\r
/**\r
* Returns the value of field 'id'.\r
- * \r
+ *\r
* @return int\r
* @return the value of field 'id'.\r
*/\r
public int getId()\r
{\r
return this._id;\r
- } //-- int getId() \r
+ } //-- int getId()\r
\r
/**\r
* Returns the value of field 'start'.\r
- * \r
+ *\r
* @return int\r
* @return the value of field 'start'.\r
*/\r
public int getStart()\r
{\r
return this._start;\r
- } //-- int getStart() \r
+ } //-- int getStart()\r
\r
/**\r
* Method hasColour\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasColour()\r
{\r
return this._has_colour;\r
- } //-- boolean hasColour() \r
+ } //-- boolean hasColour()\r
\r
/**\r
* Method hasEnd\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasEnd()\r
{\r
return this._has_end;\r
- } //-- boolean hasEnd() \r
+ } //-- boolean hasEnd()\r
\r
/**\r
* Method hasId\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasId()\r
{\r
return this._has_id;\r
- } //-- boolean hasId() \r
+ } //-- boolean hasId()\r
\r
/**\r
* Method hasStart\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasStart()\r
{\r
return this._has_start;\r
- } //-- boolean hasStart() \r
+ } //-- boolean hasStart()\r
\r
/**\r
* Method isValid\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean isValid()\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ } //-- boolean isValid()\r
\r
/**\r
* Method marshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param out\r
*/\r
public void marshal(java.io.Writer out)\r
throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- \r
+\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ } //-- void marshal(java.io.Writer)\r
\r
/**\r
* Method marshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param handler\r
*/\r
public void marshal(org.xml.sax.ContentHandler handler)\r
throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- \r
+\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ } //-- void marshal(org.xml.sax.ContentHandler)\r
\r
/**\r
* Sets the value of field 'colour'.\r
- * \r
+ *\r
* @param colour the value of field 'colour'.\r
*/\r
public void setColour(int colour)\r
{\r
this._colour = colour;\r
this._has_colour = true;\r
- } //-- void setColour(int) \r
+ } //-- void setColour(int)\r
\r
/**\r
* Sets the value of field 'end'.\r
- * \r
+ *\r
* @param end the value of field 'end'.\r
*/\r
public void setEnd(int end)\r
{\r
this._end = end;\r
this._has_end = true;\r
- } //-- void setEnd(int) \r
+ } //-- void setEnd(int)\r
\r
/**\r
* Sets the value of field 'id'.\r
- * \r
+ *\r
* @param id the value of field 'id'.\r
*/\r
public void setId(int id)\r
{\r
this._id = id;\r
this._has_id = true;\r
- } //-- void setId(int) \r
+ } //-- void setId(int)\r
\r
/**\r
* Sets the value of field 'start'.\r
- * \r
+ *\r
* @param start the value of field 'start'.\r
*/\r
public void setStart(int start)\r
{\r
this._start = start;\r
this._has_start = true;\r
- } //-- void setStart(int) \r
+ } //-- void setStart(int)\r
\r
/**\r
* Method unmarshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param reader\r
* @return Object\r
*/\r
throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
return (jalview.binding.JSeq) Unmarshaller.unmarshal(jalview.binding.JSeq.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ } //-- java.lang.Object unmarshal(java.io.Reader)\r
\r
/**\r
* Method validate\r
- * \r
+ *\r
*/\r
public void validate()\r
throws org.exolab.castor.xml.ValidationException\r
{\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ } //-- void validate()\r
\r
}\r
/*\r
- * This class was automatically generated with \r
+ * This class was automatically generated with\r
* <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.binding;\r
\r
//---------------------------------/\r
\r
/**\r
* Class JalviewModel.\r
- * \r
+ *\r
* @version $Revision$ $Date$\r
*/\r
public class JalviewModel implements java.io.Serializable {\r
\r
/**\r
* Returns the value of field 'creationDate'.\r
- * \r
+ *\r
* @return Date\r
* @return the value of field 'creationDate'.\r
*/\r
public java.util.Date getCreationDate()\r
{\r
return this._creationDate;\r
- } //-- java.util.Date getCreationDate() \r
+ } //-- java.util.Date getCreationDate()\r
\r
/**\r
* Returns the value of field 'jalviewModelSequence'.\r
- * \r
+ *\r
* @return JalviewModelSequence\r
* @return the value of field 'jalviewModelSequence'.\r
*/\r
public jalview.binding.JalviewModelSequence getJalviewModelSequence()\r
{\r
return this._jalviewModelSequence;\r
- } //-- jalview.binding.JalviewModelSequence getJalviewModelSequence() \r
+ } //-- jalview.binding.JalviewModelSequence getJalviewModelSequence()\r
\r
/**\r
* Returns the value of field 'vamsasModel'.\r
- * \r
+ *\r
* @return VamsasModel\r
* @return the value of field 'vamsasModel'.\r
*/\r
public jalview.binding.VamsasModel getVamsasModel()\r
{\r
return this._vamsasModel;\r
- } //-- jalview.binding.VamsasModel getVamsasModel() \r
+ } //-- jalview.binding.VamsasModel getVamsasModel()\r
\r
/**\r
* Method isValid\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean isValid()\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ } //-- boolean isValid()\r
\r
/**\r
* Method marshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param out\r
*/\r
public void marshal(java.io.Writer out)\r
throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- \r
+\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ } //-- void marshal(java.io.Writer)\r
\r
/**\r
* Method marshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param handler\r
*/\r
public void marshal(org.xml.sax.ContentHandler handler)\r
throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- \r
+\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ } //-- void marshal(org.xml.sax.ContentHandler)\r
\r
/**\r
* Sets the value of field 'creationDate'.\r
- * \r
+ *\r
* @param creationDate the value of field 'creationDate'.\r
*/\r
public void setCreationDate(java.util.Date creationDate)\r
{\r
this._creationDate = creationDate;\r
- } //-- void setCreationDate(java.util.Date) \r
+ } //-- void setCreationDate(java.util.Date)\r
\r
/**\r
* Sets the value of field 'jalviewModelSequence'.\r
- * \r
+ *\r
* @param jalviewModelSequence the value of field\r
* 'jalviewModelSequence'.\r
*/\r
public void setJalviewModelSequence(jalview.binding.JalviewModelSequence jalviewModelSequence)\r
{\r
this._jalviewModelSequence = jalviewModelSequence;\r
- } //-- void setJalviewModelSequence(jalview.binding.JalviewModelSequence) \r
+ } //-- void setJalviewModelSequence(jalview.binding.JalviewModelSequence)\r
\r
/**\r
* Sets the value of field 'vamsasModel'.\r
- * \r
+ *\r
* @param vamsasModel the value of field 'vamsasModel'.\r
*/\r
public void setVamsasModel(jalview.binding.VamsasModel vamsasModel)\r
{\r
this._vamsasModel = vamsasModel;\r
- } //-- void setVamsasModel(jalview.binding.VamsasModel) \r
+ } //-- void setVamsasModel(jalview.binding.VamsasModel)\r
\r
/**\r
* Method unmarshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param reader\r
* @return Object\r
*/\r
throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
return (jalview.binding.JalviewModel) Unmarshaller.unmarshal(jalview.binding.JalviewModel.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ } //-- java.lang.Object unmarshal(java.io.Reader)\r
\r
/**\r
* Method validate\r
- * \r
+ *\r
*/\r
public void validate()\r
throws org.exolab.castor.xml.ValidationException\r
{\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ } //-- void validate()\r
\r
}\r
/*\r
- * This class was automatically generated with \r
+ * This class was automatically generated with\r
* <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.binding;\r
\r
//---------------------------------/\r
\r
/**\r
* Class JalviewModelSequence.\r
- * \r
+ *\r
* @version $Revision$ $Date$\r
*/\r
public class JalviewModelSequence implements java.io.Serializable {\r
\r
/**\r
* Method addJGroup\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param vJGroup\r
*/\r
public void addJGroup(jalview.binding.JGroup vJGroup)\r
throws java.lang.IndexOutOfBoundsException\r
{\r
_JGroupList.addElement(vJGroup);\r
- } //-- void addJGroup(jalview.binding.JGroup) \r
+ } //-- void addJGroup(jalview.binding.JGroup)\r
\r
/**\r
* Method addJGroup\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @param vJGroup\r
*/\r
throws java.lang.IndexOutOfBoundsException\r
{\r
_JGroupList.insertElementAt(vJGroup, index);\r
- } //-- void addJGroup(int, jalview.binding.JGroup) \r
+ } //-- void addJGroup(int, jalview.binding.JGroup)\r
\r
/**\r
* Method addJSeq\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param vJSeq\r
*/\r
public void addJSeq(jalview.binding.JSeq vJSeq)\r
throws java.lang.IndexOutOfBoundsException\r
{\r
_JSeqList.addElement(vJSeq);\r
- } //-- void addJSeq(jalview.binding.JSeq) \r
+ } //-- void addJSeq(jalview.binding.JSeq)\r
\r
/**\r
* Method addJSeq\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @param vJSeq\r
*/\r
throws java.lang.IndexOutOfBoundsException\r
{\r
_JSeqList.insertElementAt(vJSeq, index);\r
- } //-- void addJSeq(int, jalview.binding.JSeq) \r
+ } //-- void addJSeq(int, jalview.binding.JSeq)\r
\r
/**\r
* Method addUserColours\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param vUserColours\r
*/\r
public void addUserColours(jalview.binding.UserColours vUserColours)\r
throws java.lang.IndexOutOfBoundsException\r
{\r
_userColoursList.addElement(vUserColours);\r
- } //-- void addUserColours(jalview.binding.UserColours) \r
+ } //-- void addUserColours(jalview.binding.UserColours)\r
\r
/**\r
* Method addUserColours\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @param vUserColours\r
*/\r
throws java.lang.IndexOutOfBoundsException\r
{\r
_userColoursList.insertElementAt(vUserColours, index);\r
- } //-- void addUserColours(int, jalview.binding.UserColours) \r
+ } //-- void addUserColours(int, jalview.binding.UserColours)\r
\r
/**\r
* Method addViewport\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param vViewport\r
*/\r
public void addViewport(jalview.binding.Viewport vViewport)\r
throws java.lang.IndexOutOfBoundsException\r
{\r
_viewportList.addElement(vViewport);\r
- } //-- void addViewport(jalview.binding.Viewport) \r
+ } //-- void addViewport(jalview.binding.Viewport)\r
\r
/**\r
* Method addViewport\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @param vViewport\r
*/\r
throws java.lang.IndexOutOfBoundsException\r
{\r
_viewportList.insertElementAt(vViewport, index);\r
- } //-- void addViewport(int, jalview.binding.Viewport) \r
+ } //-- void addViewport(int, jalview.binding.Viewport)\r
\r
/**\r
* Method enumerateJGroup\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return Enumeration\r
*/\r
public java.util.Enumeration enumerateJGroup()\r
{\r
return _JGroupList.elements();\r
- } //-- java.util.Enumeration enumerateJGroup() \r
+ } //-- java.util.Enumeration enumerateJGroup()\r
\r
/**\r
* Method enumerateJSeq\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return Enumeration\r
*/\r
public java.util.Enumeration enumerateJSeq()\r
{\r
return _JSeqList.elements();\r
- } //-- java.util.Enumeration enumerateJSeq() \r
+ } //-- java.util.Enumeration enumerateJSeq()\r
\r
/**\r
* Method enumerateUserColours\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return Enumeration\r
*/\r
public java.util.Enumeration enumerateUserColours()\r
{\r
return _userColoursList.elements();\r
- } //-- java.util.Enumeration enumerateUserColours() \r
+ } //-- java.util.Enumeration enumerateUserColours()\r
\r
/**\r
* Method enumerateViewport\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return Enumeration\r
*/\r
public java.util.Enumeration enumerateViewport()\r
{\r
return _viewportList.elements();\r
- } //-- java.util.Enumeration enumerateViewport() \r
+ } //-- java.util.Enumeration enumerateViewport()\r
\r
/**\r
* Method getJGroup\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @return JGroup\r
*/\r
if ((index < 0) || (index > _JGroupList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
- \r
+\r
return (jalview.binding.JGroup) _JGroupList.elementAt(index);\r
- } //-- jalview.binding.JGroup getJGroup(int) \r
+ } //-- jalview.binding.JGroup getJGroup(int)\r
\r
/**\r
* Method getJGroup\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return JGroup\r
*/\r
public jalview.binding.JGroup[] getJGroup()\r
mArray[index] = (jalview.binding.JGroup) _JGroupList.elementAt(index);\r
}\r
return mArray;\r
- } //-- jalview.binding.JGroup[] getJGroup() \r
+ } //-- jalview.binding.JGroup[] getJGroup()\r
\r
/**\r
* Method getJGroupCount\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return int\r
*/\r
public int getJGroupCount()\r
{\r
return _JGroupList.size();\r
- } //-- int getJGroupCount() \r
+ } //-- int getJGroupCount()\r
\r
/**\r
* Method getJSeq\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @return JSeq\r
*/\r
if ((index < 0) || (index > _JSeqList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
- \r
+\r
return (jalview.binding.JSeq) _JSeqList.elementAt(index);\r
- } //-- jalview.binding.JSeq getJSeq(int) \r
+ } //-- jalview.binding.JSeq getJSeq(int)\r
\r
/**\r
* Method getJSeq\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return JSeq\r
*/\r
public jalview.binding.JSeq[] getJSeq()\r
mArray[index] = (jalview.binding.JSeq) _JSeqList.elementAt(index);\r
}\r
return mArray;\r
- } //-- jalview.binding.JSeq[] getJSeq() \r
+ } //-- jalview.binding.JSeq[] getJSeq()\r
\r
/**\r
* Method getJSeqCount\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return int\r
*/\r
public int getJSeqCount()\r
{\r
return _JSeqList.size();\r
- } //-- int getJSeqCount() \r
+ } //-- int getJSeqCount()\r
\r
/**\r
* Method getUserColours\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @return UserColours\r
*/\r
if ((index < 0) || (index > _userColoursList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
- \r
+\r
return (jalview.binding.UserColours) _userColoursList.elementAt(index);\r
- } //-- jalview.binding.UserColours getUserColours(int) \r
+ } //-- jalview.binding.UserColours getUserColours(int)\r
\r
/**\r
* Method getUserColours\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return UserColours\r
*/\r
public jalview.binding.UserColours[] getUserColours()\r
mArray[index] = (jalview.binding.UserColours) _userColoursList.elementAt(index);\r
}\r
return mArray;\r
- } //-- jalview.binding.UserColours[] getUserColours() \r
+ } //-- jalview.binding.UserColours[] getUserColours()\r
\r
/**\r
* Method getUserColoursCount\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return int\r
*/\r
public int getUserColoursCount()\r
{\r
return _userColoursList.size();\r
- } //-- int getUserColoursCount() \r
+ } //-- int getUserColoursCount()\r
\r
/**\r
* Method getViewport\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @return Viewport\r
*/\r
if ((index < 0) || (index > _viewportList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
- \r
+\r
return (jalview.binding.Viewport) _viewportList.elementAt(index);\r
- } //-- jalview.binding.Viewport getViewport(int) \r
+ } //-- jalview.binding.Viewport getViewport(int)\r
\r
/**\r
* Method getViewport\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return Viewport\r
*/\r
public jalview.binding.Viewport[] getViewport()\r
mArray[index] = (jalview.binding.Viewport) _viewportList.elementAt(index);\r
}\r
return mArray;\r
- } //-- jalview.binding.Viewport[] getViewport() \r
+ } //-- jalview.binding.Viewport[] getViewport()\r
\r
/**\r
* Method getViewportCount\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return int\r
*/\r
public int getViewportCount()\r
{\r
return _viewportList.size();\r
- } //-- int getViewportCount() \r
+ } //-- int getViewportCount()\r
\r
/**\r
* Method isValid\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean isValid()\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ } //-- boolean isValid()\r
\r
/**\r
* Method marshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param out\r
*/\r
public void marshal(java.io.Writer out)\r
throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- \r
+\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ } //-- void marshal(java.io.Writer)\r
\r
/**\r
* Method marshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param handler\r
*/\r
public void marshal(org.xml.sax.ContentHandler handler)\r
throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- \r
+\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ } //-- void marshal(org.xml.sax.ContentHandler)\r
\r
/**\r
* Method removeAllJGroup\r
- * \r
+ *\r
*/\r
public void removeAllJGroup()\r
{\r
_JGroupList.removeAllElements();\r
- } //-- void removeAllJGroup() \r
+ } //-- void removeAllJGroup()\r
\r
/**\r
* Method removeAllJSeq\r
- * \r
+ *\r
*/\r
public void removeAllJSeq()\r
{\r
_JSeqList.removeAllElements();\r
- } //-- void removeAllJSeq() \r
+ } //-- void removeAllJSeq()\r
\r
/**\r
* Method removeAllUserColours\r
- * \r
+ *\r
*/\r
public void removeAllUserColours()\r
{\r
_userColoursList.removeAllElements();\r
- } //-- void removeAllUserColours() \r
+ } //-- void removeAllUserColours()\r
\r
/**\r
* Method removeAllViewport\r
- * \r
+ *\r
*/\r
public void removeAllViewport()\r
{\r
_viewportList.removeAllElements();\r
- } //-- void removeAllViewport() \r
+ } //-- void removeAllViewport()\r
\r
/**\r
* Method removeJGroup\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @return JGroup\r
*/\r
java.lang.Object obj = _JGroupList.elementAt(index);\r
_JGroupList.removeElementAt(index);\r
return (jalview.binding.JGroup) obj;\r
- } //-- jalview.binding.JGroup removeJGroup(int) \r
+ } //-- jalview.binding.JGroup removeJGroup(int)\r
\r
/**\r
* Method removeJSeq\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @return JSeq\r
*/\r
java.lang.Object obj = _JSeqList.elementAt(index);\r
_JSeqList.removeElementAt(index);\r
return (jalview.binding.JSeq) obj;\r
- } //-- jalview.binding.JSeq removeJSeq(int) \r
+ } //-- jalview.binding.JSeq removeJSeq(int)\r
\r
/**\r
* Method removeUserColours\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @return UserColours\r
*/\r
java.lang.Object obj = _userColoursList.elementAt(index);\r
_userColoursList.removeElementAt(index);\r
return (jalview.binding.UserColours) obj;\r
- } //-- jalview.binding.UserColours removeUserColours(int) \r
+ } //-- jalview.binding.UserColours removeUserColours(int)\r
\r
/**\r
* Method removeViewport\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @return Viewport\r
*/\r
java.lang.Object obj = _viewportList.elementAt(index);\r
_viewportList.removeElementAt(index);\r
return (jalview.binding.Viewport) obj;\r
- } //-- jalview.binding.Viewport removeViewport(int) \r
+ } //-- jalview.binding.Viewport removeViewport(int)\r
\r
/**\r
* Method setJGroup\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @param vJGroup\r
*/\r
throw new IndexOutOfBoundsException();\r
}\r
_JGroupList.setElementAt(vJGroup, index);\r
- } //-- void setJGroup(int, jalview.binding.JGroup) \r
+ } //-- void setJGroup(int, jalview.binding.JGroup)\r
\r
/**\r
* Method setJGroup\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param JGroupArray\r
*/\r
public void setJGroup(jalview.binding.JGroup[] JGroupArray)\r
for (int i = 0; i < JGroupArray.length; i++) {\r
_JGroupList.addElement(JGroupArray[i]);\r
}\r
- } //-- void setJGroup(jalview.binding.JGroup) \r
+ } //-- void setJGroup(jalview.binding.JGroup)\r
\r
/**\r
* Method setJSeq\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @param vJSeq\r
*/\r
throw new IndexOutOfBoundsException();\r
}\r
_JSeqList.setElementAt(vJSeq, index);\r
- } //-- void setJSeq(int, jalview.binding.JSeq) \r
+ } //-- void setJSeq(int, jalview.binding.JSeq)\r
\r
/**\r
* Method setJSeq\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param JSeqArray\r
*/\r
public void setJSeq(jalview.binding.JSeq[] JSeqArray)\r
for (int i = 0; i < JSeqArray.length; i++) {\r
_JSeqList.addElement(JSeqArray[i]);\r
}\r
- } //-- void setJSeq(jalview.binding.JSeq) \r
+ } //-- void setJSeq(jalview.binding.JSeq)\r
\r
/**\r
* Method setUserColours\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @param vUserColours\r
*/\r
throw new IndexOutOfBoundsException();\r
}\r
_userColoursList.setElementAt(vUserColours, index);\r
- } //-- void setUserColours(int, jalview.binding.UserColours) \r
+ } //-- void setUserColours(int, jalview.binding.UserColours)\r
\r
/**\r
* Method setUserColours\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param userColoursArray\r
*/\r
public void setUserColours(jalview.binding.UserColours[] userColoursArray)\r
for (int i = 0; i < userColoursArray.length; i++) {\r
_userColoursList.addElement(userColoursArray[i]);\r
}\r
- } //-- void setUserColours(jalview.binding.UserColours) \r
+ } //-- void setUserColours(jalview.binding.UserColours)\r
\r
/**\r
* Method setViewport\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @param vViewport\r
*/\r
throw new IndexOutOfBoundsException();\r
}\r
_viewportList.setElementAt(vViewport, index);\r
- } //-- void setViewport(int, jalview.binding.Viewport) \r
+ } //-- void setViewport(int, jalview.binding.Viewport)\r
\r
/**\r
* Method setViewport\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param viewportArray\r
*/\r
public void setViewport(jalview.binding.Viewport[] viewportArray)\r
for (int i = 0; i < viewportArray.length; i++) {\r
_viewportList.addElement(viewportArray[i]);\r
}\r
- } //-- void setViewport(jalview.binding.Viewport) \r
+ } //-- void setViewport(jalview.binding.Viewport)\r
\r
/**\r
* Method unmarshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param reader\r
* @return Object\r
*/\r
throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
return (jalview.binding.JalviewModelSequence) Unmarshaller.unmarshal(jalview.binding.JalviewModelSequence.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ } //-- java.lang.Object unmarshal(java.io.Reader)\r
\r
/**\r
* Method validate\r
- * \r
+ *\r
*/\r
public void validate()\r
throws org.exolab.castor.xml.ValidationException\r
{\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ } //-- void validate()\r
\r
}\r
/*\r
- * This class was automatically generated with \r
+ * This class was automatically generated with\r
* <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.binding;\r
\r
//---------------------------------/\r
\r
/**\r
* Class JalviewModelSequence2.\r
- * \r
+ *\r
* @version $Revision$ $Date$\r
*/\r
public class JalviewModelSequence2 implements java.io.Serializable {\r
\r
/**\r
* Method addJalviewModelSequence2Item\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param vJalviewModelSequence2Item\r
*/\r
public void addJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item vJalviewModelSequence2Item)\r
throws java.lang.IndexOutOfBoundsException\r
{\r
_items.addElement(vJalviewModelSequence2Item);\r
- } //-- void addJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item) \r
+ } //-- void addJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item)\r
\r
/**\r
* Method addJalviewModelSequence2Item\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @param vJalviewModelSequence2Item\r
*/\r
throws java.lang.IndexOutOfBoundsException\r
{\r
_items.insertElementAt(vJalviewModelSequence2Item, index);\r
- } //-- void addJalviewModelSequence2Item(int, jalview.binding.JalviewModelSequence2Item) \r
+ } //-- void addJalviewModelSequence2Item(int, jalview.binding.JalviewModelSequence2Item)\r
\r
/**\r
* Method enumerateJalviewModelSequence2Item\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return Enumeration\r
*/\r
public java.util.Enumeration enumerateJalviewModelSequence2Item()\r
{\r
return _items.elements();\r
- } //-- java.util.Enumeration enumerateJalviewModelSequence2Item() \r
+ } //-- java.util.Enumeration enumerateJalviewModelSequence2Item()\r
\r
/**\r
* Method getJalviewModelSequence2Item\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @return JalviewModelSequence2Item\r
*/\r
if ((index < 0) || (index > _items.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
- \r
+\r
return (jalview.binding.JalviewModelSequence2Item) _items.elementAt(index);\r
- } //-- jalview.binding.JalviewModelSequence2Item getJalviewModelSequence2Item(int) \r
+ } //-- jalview.binding.JalviewModelSequence2Item getJalviewModelSequence2Item(int)\r
\r
/**\r
* Method getJalviewModelSequence2Item\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return JalviewModelSequence2Item\r
*/\r
public jalview.binding.JalviewModelSequence2Item[] getJalviewModelSequence2Item()\r
mArray[index] = (jalview.binding.JalviewModelSequence2Item) _items.elementAt(index);\r
}\r
return mArray;\r
- } //-- jalview.binding.JalviewModelSequence2Item[] getJalviewModelSequence2Item() \r
+ } //-- jalview.binding.JalviewModelSequence2Item[] getJalviewModelSequence2Item()\r
\r
/**\r
* Method getJalviewModelSequence2ItemCount\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return int\r
*/\r
public int getJalviewModelSequence2ItemCount()\r
{\r
return _items.size();\r
- } //-- int getJalviewModelSequence2ItemCount() \r
+ } //-- int getJalviewModelSequence2ItemCount()\r
\r
/**\r
* Method isValid\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean isValid()\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ } //-- boolean isValid()\r
\r
/**\r
* Method marshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param out\r
*/\r
public void marshal(java.io.Writer out)\r
throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- \r
+\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ } //-- void marshal(java.io.Writer)\r
\r
/**\r
* Method marshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param handler\r
*/\r
public void marshal(org.xml.sax.ContentHandler handler)\r
throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- \r
+\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ } //-- void marshal(org.xml.sax.ContentHandler)\r
\r
/**\r
* Method removeAllJalviewModelSequence2Item\r
- * \r
+ *\r
*/\r
public void removeAllJalviewModelSequence2Item()\r
{\r
_items.removeAllElements();\r
- } //-- void removeAllJalviewModelSequence2Item() \r
+ } //-- void removeAllJalviewModelSequence2Item()\r
\r
/**\r
* Method removeJalviewModelSequence2Item\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @return JalviewModelSequence2Item\r
*/\r
java.lang.Object obj = _items.elementAt(index);\r
_items.removeElementAt(index);\r
return (jalview.binding.JalviewModelSequence2Item) obj;\r
- } //-- jalview.binding.JalviewModelSequence2Item removeJalviewModelSequence2Item(int) \r
+ } //-- jalview.binding.JalviewModelSequence2Item removeJalviewModelSequence2Item(int)\r
\r
/**\r
* Method setJalviewModelSequence2Item\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @param vJalviewModelSequence2Item\r
*/\r
throw new IndexOutOfBoundsException();\r
}\r
_items.setElementAt(vJalviewModelSequence2Item, index);\r
- } //-- void setJalviewModelSequence2Item(int, jalview.binding.JalviewModelSequence2Item) \r
+ } //-- void setJalviewModelSequence2Item(int, jalview.binding.JalviewModelSequence2Item)\r
\r
/**\r
* Method setJalviewModelSequence2Item\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param jalviewModelSequence2ItemArray\r
*/\r
public void setJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item[] jalviewModelSequence2ItemArray)\r
for (int i = 0; i < jalviewModelSequence2ItemArray.length; i++) {\r
_items.addElement(jalviewModelSequence2ItemArray[i]);\r
}\r
- } //-- void setJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item) \r
+ } //-- void setJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item)\r
\r
/**\r
* Method unmarshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param reader\r
* @return Object\r
*/\r
throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
return (jalview.binding.JalviewModelSequence2) Unmarshaller.unmarshal(jalview.binding.JalviewModelSequence2.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ } //-- java.lang.Object unmarshal(java.io.Reader)\r
\r
/**\r
* Method validate\r
- * \r
+ *\r
*/\r
public void validate()\r
throws org.exolab.castor.xml.ValidationException\r
{\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ } //-- void validate()\r
\r
}\r
/*\r
- * This class was automatically generated with \r
+ * This class was automatically generated with\r
* <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.binding;\r
\r
//---------------------------------/\r
\r
/**\r
* Class JalviewModelSequence2Item.\r
- * \r
+ *\r
* @version $Revision$ $Date$\r
*/\r
public class JalviewModelSequence2Item implements java.io.Serializable {\r
\r
/**\r
* Method addUserColourScheme\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param vUserColourScheme\r
*/\r
public void addUserColourScheme(jalview.binding.UserColourScheme vUserColourScheme)\r
throws java.lang.IndexOutOfBoundsException\r
{\r
_userColourSchemeList.addElement(vUserColourScheme);\r
- } //-- void addUserColourScheme(jalview.binding.UserColourScheme) \r
+ } //-- void addUserColourScheme(jalview.binding.UserColourScheme)\r
\r
/**\r
* Method addUserColourScheme\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @param vUserColourScheme\r
*/\r
throws java.lang.IndexOutOfBoundsException\r
{\r
_userColourSchemeList.insertElementAt(vUserColourScheme, index);\r
- } //-- void addUserColourScheme(int, jalview.binding.UserColourScheme) \r
+ } //-- void addUserColourScheme(int, jalview.binding.UserColourScheme)\r
\r
/**\r
* Method enumerateUserColourScheme\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return Enumeration\r
*/\r
public java.util.Enumeration enumerateUserColourScheme()\r
{\r
return _userColourSchemeList.elements();\r
- } //-- java.util.Enumeration enumerateUserColourScheme() \r
+ } //-- java.util.Enumeration enumerateUserColourScheme()\r
\r
/**\r
* Method getUserColourScheme\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @return UserColourScheme\r
*/\r
if ((index < 0) || (index > _userColourSchemeList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
- \r
+\r
return (jalview.binding.UserColourScheme) _userColourSchemeList.elementAt(index);\r
- } //-- jalview.binding.UserColourScheme getUserColourScheme(int) \r
+ } //-- jalview.binding.UserColourScheme getUserColourScheme(int)\r
\r
/**\r
* Method getUserColourScheme\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return UserColourScheme\r
*/\r
public jalview.binding.UserColourScheme[] getUserColourScheme()\r
mArray[index] = (jalview.binding.UserColourScheme) _userColourSchemeList.elementAt(index);\r
}\r
return mArray;\r
- } //-- jalview.binding.UserColourScheme[] getUserColourScheme() \r
+ } //-- jalview.binding.UserColourScheme[] getUserColourScheme()\r
\r
/**\r
* Method getUserColourSchemeCount\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return int\r
*/\r
public int getUserColourSchemeCount()\r
{\r
return _userColourSchemeList.size();\r
- } //-- int getUserColourSchemeCount() \r
+ } //-- int getUserColourSchemeCount()\r
\r
/**\r
* Method removeAllUserColourScheme\r
- * \r
+ *\r
*/\r
public void removeAllUserColourScheme()\r
{\r
_userColourSchemeList.removeAllElements();\r
- } //-- void removeAllUserColourScheme() \r
+ } //-- void removeAllUserColourScheme()\r
\r
/**\r
* Method removeUserColourScheme\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @return UserColourScheme\r
*/\r
java.lang.Object obj = _userColourSchemeList.elementAt(index);\r
_userColourSchemeList.removeElementAt(index);\r
return (jalview.binding.UserColourScheme) obj;\r
- } //-- jalview.binding.UserColourScheme removeUserColourScheme(int) \r
+ } //-- jalview.binding.UserColourScheme removeUserColourScheme(int)\r
\r
/**\r
* Method setUserColourScheme\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @param vUserColourScheme\r
*/\r
throw new IndexOutOfBoundsException();\r
}\r
_userColourSchemeList.setElementAt(vUserColourScheme, index);\r
- } //-- void setUserColourScheme(int, jalview.binding.UserColourScheme) \r
+ } //-- void setUserColourScheme(int, jalview.binding.UserColourScheme)\r
\r
/**\r
* Method setUserColourScheme\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param userColourSchemeArray\r
*/\r
public void setUserColourScheme(jalview.binding.UserColourScheme[] userColourSchemeArray)\r
for (int i = 0; i < userColourSchemeArray.length; i++) {\r
_userColourSchemeList.addElement(userColourSchemeArray[i]);\r
}\r
- } //-- void setUserColourScheme(jalview.binding.UserColourScheme) \r
+ } //-- void setUserColourScheme(jalview.binding.UserColourScheme)\r
\r
}\r
/*\r
- * This class was automatically generated with \r
+ * This class was automatically generated with\r
* <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.binding;\r
\r
//---------------------------------/\r
\r
/**\r
* Class JalviewUserColours.\r
- * \r
+ *\r
* @version $Revision$ $Date$\r
*/\r
public class JalviewUserColours implements java.io.Serializable {\r
\r
/**\r
* Method addColour\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param vColour\r
*/\r
public void addColour(jalview.binding.Colour vColour)\r
throws java.lang.IndexOutOfBoundsException\r
{\r
_colourList.addElement(vColour);\r
- } //-- void addColour(jalview.binding.Colour) \r
+ } //-- void addColour(jalview.binding.Colour)\r
\r
/**\r
* Method addColour\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @param vColour\r
*/\r
throws java.lang.IndexOutOfBoundsException\r
{\r
_colourList.insertElementAt(vColour, index);\r
- } //-- void addColour(int, jalview.binding.Colour) \r
+ } //-- void addColour(int, jalview.binding.Colour)\r
\r
/**\r
* Method enumerateColour\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return Enumeration\r
*/\r
public java.util.Enumeration enumerateColour()\r
{\r
return _colourList.elements();\r
- } //-- java.util.Enumeration enumerateColour() \r
+ } //-- java.util.Enumeration enumerateColour()\r
\r
/**\r
* Method getColour\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @return Colour\r
*/\r
if ((index < 0) || (index > _colourList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
- \r
+\r
return (jalview.binding.Colour) _colourList.elementAt(index);\r
- } //-- jalview.binding.Colour getColour(int) \r
+ } //-- jalview.binding.Colour getColour(int)\r
\r
/**\r
* Method getColour\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return Colour\r
*/\r
public jalview.binding.Colour[] getColour()\r
mArray[index] = (jalview.binding.Colour) _colourList.elementAt(index);\r
}\r
return mArray;\r
- } //-- jalview.binding.Colour[] getColour() \r
+ } //-- jalview.binding.Colour[] getColour()\r
\r
/**\r
* Method getColourCount\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return int\r
*/\r
public int getColourCount()\r
{\r
return _colourList.size();\r
- } //-- int getColourCount() \r
+ } //-- int getColourCount()\r
\r
/**\r
* Method isValid\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean isValid()\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ } //-- boolean isValid()\r
\r
/**\r
* Method marshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param out\r
*/\r
public void marshal(java.io.Writer out)\r
throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- \r
+\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ } //-- void marshal(java.io.Writer)\r
\r
/**\r
* Method marshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param handler\r
*/\r
public void marshal(org.xml.sax.ContentHandler handler)\r
throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- \r
+\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ } //-- void marshal(org.xml.sax.ContentHandler)\r
\r
/**\r
* Method removeAllColour\r
- * \r
+ *\r
*/\r
public void removeAllColour()\r
{\r
_colourList.removeAllElements();\r
- } //-- void removeAllColour() \r
+ } //-- void removeAllColour()\r
\r
/**\r
* Method removeColour\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @return Colour\r
*/\r
java.lang.Object obj = _colourList.elementAt(index);\r
_colourList.removeElementAt(index);\r
return (jalview.binding.Colour) obj;\r
- } //-- jalview.binding.Colour removeColour(int) \r
+ } //-- jalview.binding.Colour removeColour(int)\r
\r
/**\r
* Method setColour\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @param vColour\r
*/\r
throw new IndexOutOfBoundsException();\r
}\r
_colourList.setElementAt(vColour, index);\r
- } //-- void setColour(int, jalview.binding.Colour) \r
+ } //-- void setColour(int, jalview.binding.Colour)\r
\r
/**\r
* Method setColour\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param colourArray\r
*/\r
public void setColour(jalview.binding.Colour[] colourArray)\r
for (int i = 0; i < colourArray.length; i++) {\r
_colourList.addElement(colourArray[i]);\r
}\r
- } //-- void setColour(jalview.binding.Colour) \r
+ } //-- void setColour(jalview.binding.Colour)\r
\r
/**\r
* Method unmarshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param reader\r
* @return Object\r
*/\r
throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
return (jalview.binding.JalviewUserColours) Unmarshaller.unmarshal(jalview.binding.JalviewUserColours.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ } //-- java.lang.Object unmarshal(java.io.Reader)\r
\r
/**\r
* Method validate\r
- * \r
+ *\r
*/\r
public void validate()\r
throws org.exolab.castor.xml.ValidationException\r
{\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ } //-- void validate()\r
\r
}\r
/*\r
- * This class was automatically generated with \r
+ * This class was automatically generated with\r
* <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.binding;\r
\r
//---------------------------------/\r
\r
/**\r
* Class JalviewUserColoursItem.\r
- * \r
+ *\r
* @version $Revision$ $Date$\r
*/\r
public class JalviewUserColoursItem implements java.io.Serializable {\r
\r
/**\r
* Returns the value of field 'colour'.\r
- * \r
+ *\r
* @return Colour\r
* @return the value of field 'colour'.\r
*/\r
public jalview.binding.Colour getColour()\r
{\r
return this._colour;\r
- } //-- jalview.binding.Colour getColour() \r
+ } //-- jalview.binding.Colour getColour()\r
\r
/**\r
* Sets the value of field 'colour'.\r
- * \r
+ *\r
* @param colour the value of field 'colour'.\r
*/\r
public void setColour(jalview.binding.Colour colour)\r
{\r
this._colour = colour;\r
- } //-- void setColour(jalview.binding.Colour) \r
+ } //-- void setColour(jalview.binding.Colour)\r
\r
}\r
/*\r
- * This class was automatically generated with \r
+ * This class was automatically generated with\r
* <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.binding;\r
\r
//---------------------------------/\r
\r
/**\r
* Class Residue.\r
- * \r
+ *\r
* @version $Revision$ $Date$\r
*/\r
public class Residue implements java.io.Serializable {\r
\r
/**\r
* Method deleteRGB\r
- * \r
+ *\r
*/\r
public void deleteRGB()\r
{\r
this._has_RGB= false;\r
- } //-- void deleteRGB() \r
+ } //-- void deleteRGB()\r
\r
/**\r
* Returns the value of field 'name'.\r
- * \r
+ *\r
* @return String\r
* @return the value of field 'name'.\r
*/\r
public java.lang.String getName()\r
{\r
return this._name;\r
- } //-- java.lang.String getName() \r
+ } //-- java.lang.String getName()\r
\r
/**\r
* Returns the value of field 'RGB'.\r
- * \r
+ *\r
* @return int\r
* @return the value of field 'RGB'.\r
*/\r
public int getRGB()\r
{\r
return this._RGB;\r
- } //-- int getRGB() \r
+ } //-- int getRGB()\r
\r
/**\r
* Method hasRGB\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasRGB()\r
{\r
return this._has_RGB;\r
- } //-- boolean hasRGB() \r
+ } //-- boolean hasRGB()\r
\r
/**\r
* Method isValid\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean isValid()\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ } //-- boolean isValid()\r
\r
/**\r
* Method marshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param out\r
*/\r
public void marshal(java.io.Writer out)\r
throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- \r
+\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ } //-- void marshal(java.io.Writer)\r
\r
/**\r
* Method marshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param handler\r
*/\r
public void marshal(org.xml.sax.ContentHandler handler)\r
throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- \r
+\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ } //-- void marshal(org.xml.sax.ContentHandler)\r
\r
/**\r
* Sets the value of field 'name'.\r
- * \r
+ *\r
* @param name the value of field 'name'.\r
*/\r
public void setName(java.lang.String name)\r
{\r
this._name = name;\r
- } //-- void setName(java.lang.String) \r
+ } //-- void setName(java.lang.String)\r
\r
/**\r
* Sets the value of field 'RGB'.\r
- * \r
+ *\r
* @param RGB the value of field 'RGB'.\r
*/\r
public void setRGB(int RGB)\r
{\r
this._RGB = RGB;\r
this._has_RGB = true;\r
- } //-- void setRGB(int) \r
+ } //-- void setRGB(int)\r
\r
/**\r
* Method unmarshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param reader\r
* @return Object\r
*/\r
throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
return (jalview.binding.Residue) Unmarshaller.unmarshal(jalview.binding.Residue.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ } //-- java.lang.Object unmarshal(java.io.Reader)\r
\r
/**\r
* Method validate\r
- * \r
+ *\r
*/\r
public void validate()\r
throws org.exolab.castor.xml.ValidationException\r
{\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ } //-- void validate()\r
\r
}\r
/*\r
- * This class was automatically generated with \r
+ * This class was automatically generated with\r
* <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.binding;\r
\r
//---------------------------------/\r
\r
/**\r
* Class Sequence.\r
- * \r
+ *\r
* @version $Revision$ $Date$\r
*/\r
-public class Sequence extends SequenceType \r
+public class Sequence extends SequenceType\r
implements java.io.Serializable\r
{\r
\r
\r
/**\r
* Method isValid\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean isValid()\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ } //-- boolean isValid()\r
\r
/**\r
* Method marshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param out\r
*/\r
public void marshal(java.io.Writer out)\r
throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- \r
+\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ } //-- void marshal(java.io.Writer)\r
\r
/**\r
* Method marshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param handler\r
*/\r
public void marshal(org.xml.sax.ContentHandler handler)\r
throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- \r
+\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ } //-- void marshal(org.xml.sax.ContentHandler)\r
\r
/**\r
* Method unmarshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param reader\r
* @return Object\r
*/\r
throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
return (jalview.binding.Sequence) Unmarshaller.unmarshal(jalview.binding.Sequence.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ } //-- java.lang.Object unmarshal(java.io.Reader)\r
\r
/**\r
* Method validate\r
- * \r
+ *\r
*/\r
public void validate()\r
throws org.exolab.castor.xml.ValidationException\r
{\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ } //-- void validate()\r
\r
}\r
/*\r
- * This class was automatically generated with \r
+ * This class was automatically generated with\r
* <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.binding;\r
\r
//---------------------------------/\r
\r
/**\r
* Class SequenceSet.\r
- * \r
+ *\r
* @version $Revision$ $Date$\r
*/\r
public class SequenceSet implements java.io.Serializable {\r
\r
/**\r
* Method addAnnotation\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param vAnnotation\r
*/\r
public void addAnnotation(jalview.binding.Annotation vAnnotation)\r
throws java.lang.IndexOutOfBoundsException\r
{\r
_annotationList.addElement(vAnnotation);\r
- } //-- void addAnnotation(jalview.binding.Annotation) \r
+ } //-- void addAnnotation(jalview.binding.Annotation)\r
\r
/**\r
* Method addAnnotation\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @param vAnnotation\r
*/\r
throws java.lang.IndexOutOfBoundsException\r
{\r
_annotationList.insertElementAt(vAnnotation, index);\r
- } //-- void addAnnotation(int, jalview.binding.Annotation) \r
+ } //-- void addAnnotation(int, jalview.binding.Annotation)\r
\r
/**\r
* Method addSequence\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param vSequence\r
*/\r
public void addSequence(jalview.binding.Sequence vSequence)\r
throws java.lang.IndexOutOfBoundsException\r
{\r
_sequenceList.addElement(vSequence);\r
- } //-- void addSequence(jalview.binding.Sequence) \r
+ } //-- void addSequence(jalview.binding.Sequence)\r
\r
/**\r
* Method addSequence\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @param vSequence\r
*/\r
throws java.lang.IndexOutOfBoundsException\r
{\r
_sequenceList.insertElementAt(vSequence, index);\r
- } //-- void addSequence(int, jalview.binding.Sequence) \r
+ } //-- void addSequence(int, jalview.binding.Sequence)\r
\r
/**\r
* Method deleteAligned\r
- * \r
+ *\r
*/\r
public void deleteAligned()\r
{\r
this._has_aligned= false;\r
- } //-- void deleteAligned() \r
+ } //-- void deleteAligned()\r
\r
/**\r
* Method enumerateAnnotation\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return Enumeration\r
*/\r
public java.util.Enumeration enumerateAnnotation()\r
{\r
return _annotationList.elements();\r
- } //-- java.util.Enumeration enumerateAnnotation() \r
+ } //-- java.util.Enumeration enumerateAnnotation()\r
\r
/**\r
* Method enumerateSequence\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return Enumeration\r
*/\r
public java.util.Enumeration enumerateSequence()\r
{\r
return _sequenceList.elements();\r
- } //-- java.util.Enumeration enumerateSequence() \r
+ } //-- java.util.Enumeration enumerateSequence()\r
\r
/**\r
* Returns the value of field 'aligned'.\r
- * \r
+ *\r
* @return boolean\r
* @return the value of field 'aligned'.\r
*/\r
public boolean getAligned()\r
{\r
return this._aligned;\r
- } //-- boolean getAligned() \r
+ } //-- boolean getAligned()\r
\r
/**\r
* Method getAnnotation\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @return Annotation\r
*/\r
if ((index < 0) || (index > _annotationList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
- \r
+\r
return (jalview.binding.Annotation) _annotationList.elementAt(index);\r
- } //-- jalview.binding.Annotation getAnnotation(int) \r
+ } //-- jalview.binding.Annotation getAnnotation(int)\r
\r
/**\r
* Method getAnnotation\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return Annotation\r
*/\r
public jalview.binding.Annotation[] getAnnotation()\r
mArray[index] = (jalview.binding.Annotation) _annotationList.elementAt(index);\r
}\r
return mArray;\r
- } //-- jalview.binding.Annotation[] getAnnotation() \r
+ } //-- jalview.binding.Annotation[] getAnnotation()\r
\r
/**\r
* Method getAnnotationCount\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return int\r
*/\r
public int getAnnotationCount()\r
{\r
return _annotationList.size();\r
- } //-- int getAnnotationCount() \r
+ } //-- int getAnnotationCount()\r
\r
/**\r
* Returns the value of field 'gapChar'.\r
- * \r
+ *\r
* @return String\r
* @return the value of field 'gapChar'.\r
*/\r
public java.lang.String getGapChar()\r
{\r
return this._gapChar;\r
- } //-- java.lang.String getGapChar() \r
+ } //-- java.lang.String getGapChar()\r
\r
/**\r
* Method getSequence\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @return Sequence\r
*/\r
if ((index < 0) || (index > _sequenceList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
- \r
+\r
return (jalview.binding.Sequence) _sequenceList.elementAt(index);\r
- } //-- jalview.binding.Sequence getSequence(int) \r
+ } //-- jalview.binding.Sequence getSequence(int)\r
\r
/**\r
* Method getSequence\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return Sequence\r
*/\r
public jalview.binding.Sequence[] getSequence()\r
mArray[index] = (jalview.binding.Sequence) _sequenceList.elementAt(index);\r
}\r
return mArray;\r
- } //-- jalview.binding.Sequence[] getSequence() \r
+ } //-- jalview.binding.Sequence[] getSequence()\r
\r
/**\r
* Method getSequenceCount\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return int\r
*/\r
public int getSequenceCount()\r
{\r
return _sequenceList.size();\r
- } //-- int getSequenceCount() \r
+ } //-- int getSequenceCount()\r
\r
/**\r
* Method hasAligned\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasAligned()\r
{\r
return this._has_aligned;\r
- } //-- boolean hasAligned() \r
+ } //-- boolean hasAligned()\r
\r
/**\r
* Method isValid\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean isValid()\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ } //-- boolean isValid()\r
\r
/**\r
* Method marshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param out\r
*/\r
public void marshal(java.io.Writer out)\r
throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- \r
+\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ } //-- void marshal(java.io.Writer)\r
\r
/**\r
* Method marshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param handler\r
*/\r
public void marshal(org.xml.sax.ContentHandler handler)\r
throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- \r
+\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ } //-- void marshal(org.xml.sax.ContentHandler)\r
\r
/**\r
* Method removeAllAnnotation\r
- * \r
+ *\r
*/\r
public void removeAllAnnotation()\r
{\r
_annotationList.removeAllElements();\r
- } //-- void removeAllAnnotation() \r
+ } //-- void removeAllAnnotation()\r
\r
/**\r
* Method removeAllSequence\r
- * \r
+ *\r
*/\r
public void removeAllSequence()\r
{\r
_sequenceList.removeAllElements();\r
- } //-- void removeAllSequence() \r
+ } //-- void removeAllSequence()\r
\r
/**\r
* Method removeAnnotation\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @return Annotation\r
*/\r
java.lang.Object obj = _annotationList.elementAt(index);\r
_annotationList.removeElementAt(index);\r
return (jalview.binding.Annotation) obj;\r
- } //-- jalview.binding.Annotation removeAnnotation(int) \r
+ } //-- jalview.binding.Annotation removeAnnotation(int)\r
\r
/**\r
* Method removeSequence\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @return Sequence\r
*/\r
java.lang.Object obj = _sequenceList.elementAt(index);\r
_sequenceList.removeElementAt(index);\r
return (jalview.binding.Sequence) obj;\r
- } //-- jalview.binding.Sequence removeSequence(int) \r
+ } //-- jalview.binding.Sequence removeSequence(int)\r
\r
/**\r
* Sets the value of field 'aligned'.\r
- * \r
+ *\r
* @param aligned the value of field 'aligned'.\r
*/\r
public void setAligned(boolean aligned)\r
{\r
this._aligned = aligned;\r
this._has_aligned = true;\r
- } //-- void setAligned(boolean) \r
+ } //-- void setAligned(boolean)\r
\r
/**\r
* Method setAnnotation\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @param vAnnotation\r
*/\r
throw new IndexOutOfBoundsException();\r
}\r
_annotationList.setElementAt(vAnnotation, index);\r
- } //-- void setAnnotation(int, jalview.binding.Annotation) \r
+ } //-- void setAnnotation(int, jalview.binding.Annotation)\r
\r
/**\r
* Method setAnnotation\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param annotationArray\r
*/\r
public void setAnnotation(jalview.binding.Annotation[] annotationArray)\r
for (int i = 0; i < annotationArray.length; i++) {\r
_annotationList.addElement(annotationArray[i]);\r
}\r
- } //-- void setAnnotation(jalview.binding.Annotation) \r
+ } //-- void setAnnotation(jalview.binding.Annotation)\r
\r
/**\r
* Sets the value of field 'gapChar'.\r
- * \r
+ *\r
* @param gapChar the value of field 'gapChar'.\r
*/\r
public void setGapChar(java.lang.String gapChar)\r
{\r
this._gapChar = gapChar;\r
- } //-- void setGapChar(java.lang.String) \r
+ } //-- void setGapChar(java.lang.String)\r
\r
/**\r
* Method setSequence\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @param vSequence\r
*/\r
throw new IndexOutOfBoundsException();\r
}\r
_sequenceList.setElementAt(vSequence, index);\r
- } //-- void setSequence(int, jalview.binding.Sequence) \r
+ } //-- void setSequence(int, jalview.binding.Sequence)\r
\r
/**\r
* Method setSequence\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param sequenceArray\r
*/\r
public void setSequence(jalview.binding.Sequence[] sequenceArray)\r
for (int i = 0; i < sequenceArray.length; i++) {\r
_sequenceList.addElement(sequenceArray[i]);\r
}\r
- } //-- void setSequence(jalview.binding.Sequence) \r
+ } //-- void setSequence(jalview.binding.Sequence)\r
\r
/**\r
* Method unmarshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param reader\r
* @return Object\r
*/\r
throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
return (jalview.binding.SequenceSet) Unmarshaller.unmarshal(jalview.binding.SequenceSet.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ } //-- java.lang.Object unmarshal(java.io.Reader)\r
\r
/**\r
* Method validate\r
- * \r
+ *\r
*/\r
public void validate()\r
throws org.exolab.castor.xml.ValidationException\r
{\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ } //-- void validate()\r
\r
}\r
/*\r
- * This class was automatically generated with \r
+ * This class was automatically generated with\r
* <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.binding;\r
\r
//---------------------------------/\r
\r
/**\r
* Class SequenceType.\r
- * \r
+ *\r
* @version $Revision$ $Date$\r
*/\r
public class SequenceType implements java.io.Serializable {\r
\r
/**\r
* Returns the value of field 'id'.\r
- * \r
+ *\r
* @return String\r
* @return the value of field 'id'.\r
*/\r
public java.lang.String getId()\r
{\r
return this._id;\r
- } //-- java.lang.String getId() \r
+ } //-- java.lang.String getId()\r
\r
/**\r
* Returns the value of field 'name'.\r
- * \r
+ *\r
* @return String\r
* @return the value of field 'name'.\r
*/\r
public java.lang.String getName()\r
{\r
return this._name;\r
- } //-- java.lang.String getName() \r
+ } //-- java.lang.String getName()\r
\r
/**\r
* Returns the value of field 'sequence'.\r
- * \r
+ *\r
* @return String\r
* @return the value of field 'sequence'.\r
*/\r
public java.lang.String getSequence()\r
{\r
return this._sequence;\r
- } //-- java.lang.String getSequence() \r
+ } //-- java.lang.String getSequence()\r
\r
/**\r
* Method isValid\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean isValid()\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ } //-- boolean isValid()\r
\r
/**\r
* Method marshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param out\r
*/\r
public void marshal(java.io.Writer out)\r
throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- \r
+\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ } //-- void marshal(java.io.Writer)\r
\r
/**\r
* Method marshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param handler\r
*/\r
public void marshal(org.xml.sax.ContentHandler handler)\r
throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- \r
+\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ } //-- void marshal(org.xml.sax.ContentHandler)\r
\r
/**\r
* Sets the value of field 'id'.\r
- * \r
+ *\r
* @param id the value of field 'id'.\r
*/\r
public void setId(java.lang.String id)\r
{\r
this._id = id;\r
- } //-- void setId(java.lang.String) \r
+ } //-- void setId(java.lang.String)\r
\r
/**\r
* Sets the value of field 'name'.\r
- * \r
+ *\r
* @param name the value of field 'name'.\r
*/\r
public void setName(java.lang.String name)\r
{\r
this._name = name;\r
- } //-- void setName(java.lang.String) \r
+ } //-- void setName(java.lang.String)\r
\r
/**\r
* Sets the value of field 'sequence'.\r
- * \r
+ *\r
* @param sequence the value of field 'sequence'.\r
*/\r
public void setSequence(java.lang.String sequence)\r
{\r
this._sequence = sequence;\r
- } //-- void setSequence(java.lang.String) \r
+ } //-- void setSequence(java.lang.String)\r
\r
/**\r
* Method unmarshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param reader\r
* @return Object\r
*/\r
throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
return (jalview.binding.SequenceType) Unmarshaller.unmarshal(jalview.binding.SequenceType.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ } //-- java.lang.Object unmarshal(java.io.Reader)\r
\r
/**\r
* Method validate\r
- * \r
+ *\r
*/\r
public void validate()\r
throws org.exolab.castor.xml.ValidationException\r
{\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ } //-- void validate()\r
\r
}\r
/*\r
- * This class was automatically generated with \r
+ * This class was automatically generated with\r
* <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.binding;\r
\r
//---------------------------------/\r
\r
/**\r
* Class UserColour.\r
- * \r
+ *\r
* @version $Revision$ $Date$\r
*/\r
public class UserColour implements java.io.Serializable {\r
\r
/**\r
* Method deleteId\r
- * \r
+ *\r
*/\r
public void deleteId()\r
{\r
this._has_id= false;\r
- } //-- void deleteId() \r
+ } //-- void deleteId()\r
\r
/**\r
* Returns the value of field 'id'.\r
- * \r
+ *\r
* @return int\r
* @return the value of field 'id'.\r
*/\r
public int getId()\r
{\r
return this._id;\r
- } //-- int getId() \r
+ } //-- int getId()\r
\r
/**\r
* Returns the value of field 'userColourScheme'.\r
- * \r
+ *\r
* @return UserColourScheme\r
* @return the value of field 'userColourScheme'.\r
*/\r
public jalview.binding.UserColourScheme getUserColourScheme()\r
{\r
return this._userColourScheme;\r
- } //-- jalview.binding.UserColourScheme getUserColourScheme() \r
+ } //-- jalview.binding.UserColourScheme getUserColourScheme()\r
\r
/**\r
* Method hasId\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasId()\r
{\r
return this._has_id;\r
- } //-- boolean hasId() \r
+ } //-- boolean hasId()\r
\r
/**\r
* Method isValid\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean isValid()\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ } //-- boolean isValid()\r
\r
/**\r
* Method marshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param out\r
*/\r
public void marshal(java.io.Writer out)\r
throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- \r
+\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ } //-- void marshal(java.io.Writer)\r
\r
/**\r
* Method marshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param handler\r
*/\r
public void marshal(org.xml.sax.ContentHandler handler)\r
throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- \r
+\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ } //-- void marshal(org.xml.sax.ContentHandler)\r
\r
/**\r
* Sets the value of field 'id'.\r
- * \r
+ *\r
* @param id the value of field 'id'.\r
*/\r
public void setId(int id)\r
{\r
this._id = id;\r
this._has_id = true;\r
- } //-- void setId(int) \r
+ } //-- void setId(int)\r
\r
/**\r
* Sets the value of field 'userColourScheme'.\r
- * \r
+ *\r
* @param userColourScheme the value of field 'userColourScheme'\r
*/\r
public void setUserColourScheme(jalview.binding.UserColourScheme userColourScheme)\r
{\r
this._userColourScheme = userColourScheme;\r
- } //-- void setUserColourScheme(jalview.binding.UserColourScheme) \r
+ } //-- void setUserColourScheme(jalview.binding.UserColourScheme)\r
\r
/**\r
* Method unmarshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param reader\r
* @return Object\r
*/\r
throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
return (jalview.binding.UserColour) Unmarshaller.unmarshal(jalview.binding.UserColour.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ } //-- java.lang.Object unmarshal(java.io.Reader)\r
\r
/**\r
* Method validate\r
- * \r
+ *\r
*/\r
public void validate()\r
throws org.exolab.castor.xml.ValidationException\r
{\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ } //-- void validate()\r
\r
}\r
/*\r
- * This class was automatically generated with \r
+ * This class was automatically generated with\r
* <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.binding;\r
\r
//---------------------------------/\r
\r
/**\r
* Class UserColourScheme.\r
- * \r
+ *\r
* @version $Revision$ $Date$\r
*/\r
-public class UserColourScheme extends JalviewUserColours \r
+public class UserColourScheme extends JalviewUserColours\r
implements java.io.Serializable\r
{\r
\r
\r
/**\r
* Method isValid\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean isValid()\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ } //-- boolean isValid()\r
\r
/**\r
* Method marshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param out\r
*/\r
public void marshal(java.io.Writer out)\r
throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- \r
+\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ } //-- void marshal(java.io.Writer)\r
\r
/**\r
* Method marshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param handler\r
*/\r
public void marshal(org.xml.sax.ContentHandler handler)\r
throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- \r
+\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ } //-- void marshal(org.xml.sax.ContentHandler)\r
\r
/**\r
* Method unmarshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param reader\r
* @return Object\r
*/\r
throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
return (jalview.binding.UserColourScheme) Unmarshaller.unmarshal(jalview.binding.UserColourScheme.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ } //-- java.lang.Object unmarshal(java.io.Reader)\r
\r
/**\r
* Method validate\r
- * \r
+ *\r
*/\r
public void validate()\r
throws org.exolab.castor.xml.ValidationException\r
{\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ } //-- void validate()\r
\r
}\r
/*\r
- * This class was automatically generated with \r
+ * This class was automatically generated with\r
* <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.binding;\r
\r
//---------------------------------/\r
\r
/**\r
* Class UserColours.\r
- * \r
+ *\r
* @version $Revision$ $Date$\r
*/\r
public class UserColours implements java.io.Serializable {\r
\r
/**\r
* Returns the value of field 'id'.\r
- * \r
+ *\r
* @return String\r
* @return the value of field 'id'.\r
*/\r
public java.lang.String getId()\r
{\r
return this._id;\r
- } //-- java.lang.String getId() \r
+ } //-- java.lang.String getId()\r
\r
/**\r
* Returns the value of field 'userColourScheme'.\r
- * \r
+ *\r
* @return UserColourScheme\r
* @return the value of field 'userColourScheme'.\r
*/\r
public jalview.binding.UserColourScheme getUserColourScheme()\r
{\r
return this._userColourScheme;\r
- } //-- jalview.binding.UserColourScheme getUserColourScheme() \r
+ } //-- jalview.binding.UserColourScheme getUserColourScheme()\r
\r
/**\r
* Method isValid\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean isValid()\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ } //-- boolean isValid()\r
\r
/**\r
* Method marshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param out\r
*/\r
public void marshal(java.io.Writer out)\r
throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- \r
+\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ } //-- void marshal(java.io.Writer)\r
\r
/**\r
* Method marshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param handler\r
*/\r
public void marshal(org.xml.sax.ContentHandler handler)\r
throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- \r
+\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ } //-- void marshal(org.xml.sax.ContentHandler)\r
\r
/**\r
* Sets the value of field 'id'.\r
- * \r
+ *\r
* @param id the value of field 'id'.\r
*/\r
public void setId(java.lang.String id)\r
{\r
this._id = id;\r
- } //-- void setId(java.lang.String) \r
+ } //-- void setId(java.lang.String)\r
\r
/**\r
* Sets the value of field 'userColourScheme'.\r
- * \r
+ *\r
* @param userColourScheme the value of field 'userColourScheme'\r
*/\r
public void setUserColourScheme(jalview.binding.UserColourScheme userColourScheme)\r
{\r
this._userColourScheme = userColourScheme;\r
- } //-- void setUserColourScheme(jalview.binding.UserColourScheme) \r
+ } //-- void setUserColourScheme(jalview.binding.UserColourScheme)\r
\r
/**\r
* Method unmarshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param reader\r
* @return Object\r
*/\r
throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
return (jalview.binding.UserColours) Unmarshaller.unmarshal(jalview.binding.UserColours.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ } //-- java.lang.Object unmarshal(java.io.Reader)\r
\r
/**\r
* Method validate\r
- * \r
+ *\r
*/\r
public void validate()\r
throws org.exolab.castor.xml.ValidationException\r
{\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ } //-- void validate()\r
\r
}\r
/*\r
- * This class was automatically generated with \r
+ * This class was automatically generated with\r
* <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.binding;\r
\r
//---------------------------------/\r
\r
/**\r
* Class VAMSAS.\r
- * \r
+ *\r
* @version $Revision$ $Date$\r
*/\r
public class VAMSAS implements java.io.Serializable {\r
\r
/**\r
* Method addAlignment\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param vAlignment\r
*/\r
public void addAlignment(jalview.binding.Alignment vAlignment)\r
throws java.lang.IndexOutOfBoundsException\r
{\r
_alignmentList.addElement(vAlignment);\r
- } //-- void addAlignment(jalview.binding.Alignment) \r
+ } //-- void addAlignment(jalview.binding.Alignment)\r
\r
/**\r
* Method addAlignment\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @param vAlignment\r
*/\r
throws java.lang.IndexOutOfBoundsException\r
{\r
_alignmentList.insertElementAt(vAlignment, index);\r
- } //-- void addAlignment(int, jalview.binding.Alignment) \r
+ } //-- void addAlignment(int, jalview.binding.Alignment)\r
\r
/**\r
* Method addSequenceSet\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param vSequenceSet\r
*/\r
public void addSequenceSet(jalview.binding.SequenceSet vSequenceSet)\r
throws java.lang.IndexOutOfBoundsException\r
{\r
_sequenceSetList.addElement(vSequenceSet);\r
- } //-- void addSequenceSet(jalview.binding.SequenceSet) \r
+ } //-- void addSequenceSet(jalview.binding.SequenceSet)\r
\r
/**\r
* Method addSequenceSet\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @param vSequenceSet\r
*/\r
throws java.lang.IndexOutOfBoundsException\r
{\r
_sequenceSetList.insertElementAt(vSequenceSet, index);\r
- } //-- void addSequenceSet(int, jalview.binding.SequenceSet) \r
+ } //-- void addSequenceSet(int, jalview.binding.SequenceSet)\r
\r
/**\r
* Method addTree\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param vTree\r
*/\r
public void addTree(java.lang.String vTree)\r
throws java.lang.IndexOutOfBoundsException\r
{\r
_treeList.addElement(vTree);\r
- } //-- void addTree(java.lang.String) \r
+ } //-- void addTree(java.lang.String)\r
\r
/**\r
* Method addTree\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @param vTree\r
*/\r
throws java.lang.IndexOutOfBoundsException\r
{\r
_treeList.insertElementAt(vTree, index);\r
- } //-- void addTree(int, java.lang.String) \r
+ } //-- void addTree(int, java.lang.String)\r
\r
/**\r
* Method enumerateAlignment\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return Enumeration\r
*/\r
public java.util.Enumeration enumerateAlignment()\r
{\r
return _alignmentList.elements();\r
- } //-- java.util.Enumeration enumerateAlignment() \r
+ } //-- java.util.Enumeration enumerateAlignment()\r
\r
/**\r
* Method enumerateSequenceSet\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return Enumeration\r
*/\r
public java.util.Enumeration enumerateSequenceSet()\r
{\r
return _sequenceSetList.elements();\r
- } //-- java.util.Enumeration enumerateSequenceSet() \r
+ } //-- java.util.Enumeration enumerateSequenceSet()\r
\r
/**\r
* Method enumerateTree\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return Enumeration\r
*/\r
public java.util.Enumeration enumerateTree()\r
{\r
return _treeList.elements();\r
- } //-- java.util.Enumeration enumerateTree() \r
+ } //-- java.util.Enumeration enumerateTree()\r
\r
/**\r
* Method getAlignment\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @return Alignment\r
*/\r
if ((index < 0) || (index > _alignmentList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
- \r
+\r
return (jalview.binding.Alignment) _alignmentList.elementAt(index);\r
- } //-- jalview.binding.Alignment getAlignment(int) \r
+ } //-- jalview.binding.Alignment getAlignment(int)\r
\r
/**\r
* Method getAlignment\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return Alignment\r
*/\r
public jalview.binding.Alignment[] getAlignment()\r
mArray[index] = (jalview.binding.Alignment) _alignmentList.elementAt(index);\r
}\r
return mArray;\r
- } //-- jalview.binding.Alignment[] getAlignment() \r
+ } //-- jalview.binding.Alignment[] getAlignment()\r
\r
/**\r
* Method getAlignmentCount\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return int\r
*/\r
public int getAlignmentCount()\r
{\r
return _alignmentList.size();\r
- } //-- int getAlignmentCount() \r
+ } //-- int getAlignmentCount()\r
\r
/**\r
* Method getSequenceSet\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @return SequenceSet\r
*/\r
if ((index < 0) || (index > _sequenceSetList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
- \r
+\r
return (jalview.binding.SequenceSet) _sequenceSetList.elementAt(index);\r
- } //-- jalview.binding.SequenceSet getSequenceSet(int) \r
+ } //-- jalview.binding.SequenceSet getSequenceSet(int)\r
\r
/**\r
* Method getSequenceSet\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return SequenceSet\r
*/\r
public jalview.binding.SequenceSet[] getSequenceSet()\r
mArray[index] = (jalview.binding.SequenceSet) _sequenceSetList.elementAt(index);\r
}\r
return mArray;\r
- } //-- jalview.binding.SequenceSet[] getSequenceSet() \r
+ } //-- jalview.binding.SequenceSet[] getSequenceSet()\r
\r
/**\r
* Method getSequenceSetCount\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return int\r
*/\r
public int getSequenceSetCount()\r
{\r
return _sequenceSetList.size();\r
- } //-- int getSequenceSetCount() \r
+ } //-- int getSequenceSetCount()\r
\r
/**\r
* Method getTree\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @return String\r
*/\r
if ((index < 0) || (index > _treeList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
- \r
+\r
return (String)_treeList.elementAt(index);\r
- } //-- java.lang.String getTree(int) \r
+ } //-- java.lang.String getTree(int)\r
\r
/**\r
* Method getTree\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return String\r
*/\r
public java.lang.String[] getTree()\r
mArray[index] = (String)_treeList.elementAt(index);\r
}\r
return mArray;\r
- } //-- java.lang.String[] getTree() \r
+ } //-- java.lang.String[] getTree()\r
\r
/**\r
* Method getTreeCount\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return int\r
*/\r
public int getTreeCount()\r
{\r
return _treeList.size();\r
- } //-- int getTreeCount() \r
+ } //-- int getTreeCount()\r
\r
/**\r
* Method isValid\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean isValid()\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ } //-- boolean isValid()\r
\r
/**\r
* Method marshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param out\r
*/\r
public void marshal(java.io.Writer out)\r
throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- \r
+\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ } //-- void marshal(java.io.Writer)\r
\r
/**\r
* Method marshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param handler\r
*/\r
public void marshal(org.xml.sax.ContentHandler handler)\r
throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- \r
+\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ } //-- void marshal(org.xml.sax.ContentHandler)\r
\r
/**\r
* Method removeAlignment\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @return Alignment\r
*/\r
java.lang.Object obj = _alignmentList.elementAt(index);\r
_alignmentList.removeElementAt(index);\r
return (jalview.binding.Alignment) obj;\r
- } //-- jalview.binding.Alignment removeAlignment(int) \r
+ } //-- jalview.binding.Alignment removeAlignment(int)\r
\r
/**\r
* Method removeAllAlignment\r
- * \r
+ *\r
*/\r
public void removeAllAlignment()\r
{\r
_alignmentList.removeAllElements();\r
- } //-- void removeAllAlignment() \r
+ } //-- void removeAllAlignment()\r
\r
/**\r
* Method removeAllSequenceSet\r
- * \r
+ *\r
*/\r
public void removeAllSequenceSet()\r
{\r
_sequenceSetList.removeAllElements();\r
- } //-- void removeAllSequenceSet() \r
+ } //-- void removeAllSequenceSet()\r
\r
/**\r
* Method removeAllTree\r
- * \r
+ *\r
*/\r
public void removeAllTree()\r
{\r
_treeList.removeAllElements();\r
- } //-- void removeAllTree() \r
+ } //-- void removeAllTree()\r
\r
/**\r
* Method removeSequenceSet\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @return SequenceSet\r
*/\r
java.lang.Object obj = _sequenceSetList.elementAt(index);\r
_sequenceSetList.removeElementAt(index);\r
return (jalview.binding.SequenceSet) obj;\r
- } //-- jalview.binding.SequenceSet removeSequenceSet(int) \r
+ } //-- jalview.binding.SequenceSet removeSequenceSet(int)\r
\r
/**\r
* Method removeTree\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @return String\r
*/\r
java.lang.Object obj = _treeList.elementAt(index);\r
_treeList.removeElementAt(index);\r
return (String)obj;\r
- } //-- java.lang.String removeTree(int) \r
+ } //-- java.lang.String removeTree(int)\r
\r
/**\r
* Method setAlignment\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @param vAlignment\r
*/\r
throw new IndexOutOfBoundsException();\r
}\r
_alignmentList.setElementAt(vAlignment, index);\r
- } //-- void setAlignment(int, jalview.binding.Alignment) \r
+ } //-- void setAlignment(int, jalview.binding.Alignment)\r
\r
/**\r
* Method setAlignment\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param alignmentArray\r
*/\r
public void setAlignment(jalview.binding.Alignment[] alignmentArray)\r
for (int i = 0; i < alignmentArray.length; i++) {\r
_alignmentList.addElement(alignmentArray[i]);\r
}\r
- } //-- void setAlignment(jalview.binding.Alignment) \r
+ } //-- void setAlignment(jalview.binding.Alignment)\r
\r
/**\r
* Method setSequenceSet\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @param vSequenceSet\r
*/\r
throw new IndexOutOfBoundsException();\r
}\r
_sequenceSetList.setElementAt(vSequenceSet, index);\r
- } //-- void setSequenceSet(int, jalview.binding.SequenceSet) \r
+ } //-- void setSequenceSet(int, jalview.binding.SequenceSet)\r
\r
/**\r
* Method setSequenceSet\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param sequenceSetArray\r
*/\r
public void setSequenceSet(jalview.binding.SequenceSet[] sequenceSetArray)\r
for (int i = 0; i < sequenceSetArray.length; i++) {\r
_sequenceSetList.addElement(sequenceSetArray[i]);\r
}\r
- } //-- void setSequenceSet(jalview.binding.SequenceSet) \r
+ } //-- void setSequenceSet(jalview.binding.SequenceSet)\r
\r
/**\r
* Method setTree\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @param vTree\r
*/\r
throw new IndexOutOfBoundsException();\r
}\r
_treeList.setElementAt(vTree, index);\r
- } //-- void setTree(int, java.lang.String) \r
+ } //-- void setTree(int, java.lang.String)\r
\r
/**\r
* Method setTree\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param treeArray\r
*/\r
public void setTree(java.lang.String[] treeArray)\r
for (int i = 0; i < treeArray.length; i++) {\r
_treeList.addElement(treeArray[i]);\r
}\r
- } //-- void setTree(java.lang.String) \r
+ } //-- void setTree(java.lang.String)\r
\r
/**\r
* Method unmarshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param reader\r
* @return Object\r
*/\r
throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
return (jalview.binding.VAMSAS) Unmarshaller.unmarshal(jalview.binding.VAMSAS.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ } //-- java.lang.Object unmarshal(java.io.Reader)\r
\r
/**\r
* Method validate\r
- * \r
+ *\r
*/\r
public void validate()\r
throws org.exolab.castor.xml.ValidationException\r
{\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ } //-- void validate()\r
\r
}\r
/*\r
- * This class was automatically generated with \r
+ * This class was automatically generated with\r
* <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.binding;\r
\r
//---------------------------------/\r
\r
/**\r
* Class VamsasModel.\r
- * \r
+ *\r
* @version $Revision$ $Date$\r
*/\r
-public class VamsasModel extends VAMSAS \r
+public class VamsasModel extends VAMSAS\r
implements java.io.Serializable\r
{\r
\r
\r
/**\r
* Method isValid\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean isValid()\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ } //-- boolean isValid()\r
\r
/**\r
* Method marshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param out\r
*/\r
public void marshal(java.io.Writer out)\r
throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- \r
+\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ } //-- void marshal(java.io.Writer)\r
\r
/**\r
* Method marshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param handler\r
*/\r
public void marshal(org.xml.sax.ContentHandler handler)\r
throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- \r
+\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ } //-- void marshal(org.xml.sax.ContentHandler)\r
\r
/**\r
* Method unmarshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param reader\r
* @return Object\r
*/\r
throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
return (jalview.binding.VamsasModel) Unmarshaller.unmarshal(jalview.binding.VamsasModel.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ } //-- java.lang.Object unmarshal(java.io.Reader)\r
\r
/**\r
* Method validate\r
- * \r
+ *\r
*/\r
public void validate()\r
throws org.exolab.castor.xml.ValidationException\r
{\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ } //-- void validate()\r
\r
}\r
/*\r
- * This class was automatically generated with \r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
+/*\r
+ * This class was automatically generated with\r
* <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
\r
+\r
package jalview.binding;\r
\r
//---------------------------------/\r
\r
/**\r
* Class Viewport.\r
- * \r
+ *\r
* @version $Revision$ $Date$\r
*/\r
public class Viewport implements java.io.Serializable {\r
\r
/**\r
* Method deleteConsThreshold\r
- * \r
+ *\r
*/\r
public void deleteConsThreshold()\r
{\r
this._has_consThreshold= false;\r
- } //-- void deleteConsThreshold() \r
+ } //-- void deleteConsThreshold()\r
\r
/**\r
* Method deleteConservationSelected\r
- * \r
+ *\r
*/\r
public void deleteConservationSelected()\r
{\r
this._has_conservationSelected= false;\r
- } //-- void deleteConservationSelected() \r
+ } //-- void deleteConservationSelected()\r
\r
/**\r
* Method deleteFontSize\r
- * \r
+ *\r
*/\r
public void deleteFontSize()\r
{\r
this._has_fontSize= false;\r
- } //-- void deleteFontSize() \r
+ } //-- void deleteFontSize()\r
\r
/**\r
* Method deleteFontStyle\r
- * \r
+ *\r
*/\r
public void deleteFontStyle()\r
{\r
this._has_fontStyle= false;\r
- } //-- void deleteFontStyle() \r
+ } //-- void deleteFontStyle()\r
\r
/**\r
* Method deleteHeight\r
- * \r
+ *\r
*/\r
public void deleteHeight()\r
{\r
this._has_height= false;\r
- } //-- void deleteHeight() \r
+ } //-- void deleteHeight()\r
\r
/**\r
* Method deletePidSelected\r
- * \r
+ *\r
*/\r
public void deletePidSelected()\r
{\r
this._has_pidSelected= false;\r
- } //-- void deletePidSelected() \r
+ } //-- void deletePidSelected()\r
\r
/**\r
* Method deletePidThreshold\r
- * \r
+ *\r
*/\r
public void deletePidThreshold()\r
{\r
this._has_pidThreshold= false;\r
- } //-- void deletePidThreshold() \r
+ } //-- void deletePidThreshold()\r
\r
/**\r
* Method deleteRenderGaps\r
- * \r
+ *\r
*/\r
public void deleteRenderGaps()\r
{\r
this._has_renderGaps= false;\r
- } //-- void deleteRenderGaps() \r
+ } //-- void deleteRenderGaps()\r
\r
/**\r
* Method deleteShowAnnotation\r
- * \r
+ *\r
*/\r
public void deleteShowAnnotation()\r
{\r
this._has_showAnnotation= false;\r
- } //-- void deleteShowAnnotation() \r
+ } //-- void deleteShowAnnotation()\r
\r
/**\r
* Method deleteShowBoxes\r
- * \r
+ *\r
*/\r
public void deleteShowBoxes()\r
{\r
this._has_showBoxes= false;\r
- } //-- void deleteShowBoxes() \r
+ } //-- void deleteShowBoxes()\r
\r
/**\r
* Method deleteShowColourText\r
- * \r
+ *\r
*/\r
public void deleteShowColourText()\r
{\r
this._has_showColourText= false;\r
- } //-- void deleteShowColourText() \r
+ } //-- void deleteShowColourText()\r
\r
/**\r
* Method deleteShowConservation\r
- * \r
+ *\r
*/\r
public void deleteShowConservation()\r
{\r
this._has_showConservation= false;\r
- } //-- void deleteShowConservation() \r
+ } //-- void deleteShowConservation()\r
\r
/**\r
* Method deleteShowFullId\r
- * \r
+ *\r
*/\r
public void deleteShowFullId()\r
{\r
this._has_showFullId= false;\r
- } //-- void deleteShowFullId() \r
+ } //-- void deleteShowFullId()\r
\r
/**\r
* Method deleteShowIdentity\r
- * \r
+ *\r
*/\r
public void deleteShowIdentity()\r
{\r
this._has_showIdentity= false;\r
- } //-- void deleteShowIdentity() \r
+ } //-- void deleteShowIdentity()\r
\r
/**\r
* Method deleteShowQuality\r
- * \r
+ *\r
*/\r
public void deleteShowQuality()\r
{\r
this._has_showQuality= false;\r
- } //-- void deleteShowQuality() \r
+ } //-- void deleteShowQuality()\r
\r
/**\r
* Method deleteShowSequenceFeatures\r
- * \r
+ *\r
*/\r
public void deleteShowSequenceFeatures()\r
{\r
this._has_showSequenceFeatures= false;\r
- } //-- void deleteShowSequenceFeatures() \r
+ } //-- void deleteShowSequenceFeatures()\r
\r
/**\r
* Method deleteShowText\r
- * \r
+ *\r
*/\r
public void deleteShowText()\r
{\r
this._has_showText= false;\r
- } //-- void deleteShowText() \r
+ } //-- void deleteShowText()\r
\r
/**\r
* Method deleteStartRes\r
- * \r
+ *\r
*/\r
public void deleteStartRes()\r
{\r
this._has_startRes= false;\r
- } //-- void deleteStartRes() \r
+ } //-- void deleteStartRes()\r
\r
/**\r
* Method deleteStartSeq\r
- * \r
+ *\r
*/\r
public void deleteStartSeq()\r
{\r
this._has_startSeq= false;\r
- } //-- void deleteStartSeq() \r
+ } //-- void deleteStartSeq()\r
\r
/**\r
* Method deleteWidth\r
- * \r
+ *\r
*/\r
public void deleteWidth()\r
{\r
this._has_width= false;\r
- } //-- void deleteWidth() \r
+ } //-- void deleteWidth()\r
\r
/**\r
* Method deleteWrapAlignment\r
- * \r
+ *\r
*/\r
public void deleteWrapAlignment()\r
{\r
this._has_wrapAlignment= false;\r
- } //-- void deleteWrapAlignment() \r
+ } //-- void deleteWrapAlignment()\r
\r
/**\r
* Method deleteXpos\r
- * \r
+ *\r
*/\r
public void deleteXpos()\r
{\r
this._has_xpos= false;\r
- } //-- void deleteXpos() \r
+ } //-- void deleteXpos()\r
\r
/**\r
* Method deleteYpos\r
- * \r
+ *\r
*/\r
public void deleteYpos()\r
{\r
this._has_ypos= false;\r
- } //-- void deleteYpos() \r
+ } //-- void deleteYpos()\r
\r
/**\r
* Returns the value of field 'bgColour'.\r
- * \r
+ *\r
* @return String\r
* @return the value of field 'bgColour'.\r
*/\r
public java.lang.String getBgColour()\r
{\r
return this._bgColour;\r
- } //-- java.lang.String getBgColour() \r
+ } //-- java.lang.String getBgColour()\r
\r
/**\r
* Returns the value of field 'consThreshold'.\r
- * \r
+ *\r
* @return int\r
* @return the value of field 'consThreshold'.\r
*/\r
public int getConsThreshold()\r
{\r
return this._consThreshold;\r
- } //-- int getConsThreshold() \r
+ } //-- int getConsThreshold()\r
\r
/**\r
* Returns the value of field 'conservationSelected'.\r
- * \r
+ *\r
* @return boolean\r
* @return the value of field 'conservationSelected'.\r
*/\r
public boolean getConservationSelected()\r
{\r
return this._conservationSelected;\r
- } //-- boolean getConservationSelected() \r
+ } //-- boolean getConservationSelected()\r
\r
/**\r
* Returns the value of field 'fontName'.\r
- * \r
+ *\r
* @return String\r
* @return the value of field 'fontName'.\r
*/\r
public java.lang.String getFontName()\r
{\r
return this._fontName;\r
- } //-- java.lang.String getFontName() \r
+ } //-- java.lang.String getFontName()\r
\r
/**\r
* Returns the value of field 'fontSize'.\r
- * \r
+ *\r
* @return int\r
* @return the value of field 'fontSize'.\r
*/\r
public int getFontSize()\r
{\r
return this._fontSize;\r
- } //-- int getFontSize() \r
+ } //-- int getFontSize()\r
\r
/**\r
* Returns the value of field 'fontStyle'.\r
- * \r
+ *\r
* @return int\r
* @return the value of field 'fontStyle'.\r
*/\r
public int getFontStyle()\r
{\r
return this._fontStyle;\r
- } //-- int getFontStyle() \r
+ } //-- int getFontStyle()\r
\r
/**\r
* Returns the value of field 'height'.\r
- * \r
+ *\r
* @return int\r
* @return the value of field 'height'.\r
*/\r
public int getHeight()\r
{\r
return this._height;\r
- } //-- int getHeight() \r
+ } //-- int getHeight()\r
\r
/**\r
* Returns the value of field 'pidSelected'.\r
- * \r
+ *\r
* @return boolean\r
* @return the value of field 'pidSelected'.\r
*/\r
public boolean getPidSelected()\r
{\r
return this._pidSelected;\r
- } //-- boolean getPidSelected() \r
+ } //-- boolean getPidSelected()\r
\r
/**\r
* Returns the value of field 'pidThreshold'.\r
- * \r
+ *\r
* @return int\r
* @return the value of field 'pidThreshold'.\r
*/\r
public int getPidThreshold()\r
{\r
return this._pidThreshold;\r
- } //-- int getPidThreshold() \r
+ } //-- int getPidThreshold()\r
\r
/**\r
* Returns the value of field 'renderGaps'.\r
- * \r
+ *\r
* @return boolean\r
* @return the value of field 'renderGaps'.\r
*/\r
public boolean getRenderGaps()\r
{\r
return this._renderGaps;\r
- } //-- boolean getRenderGaps() \r
+ } //-- boolean getRenderGaps()\r
\r
/**\r
* Returns the value of field 'showAnnotation'.\r
- * \r
+ *\r
* @return boolean\r
* @return the value of field 'showAnnotation'.\r
*/\r
public boolean getShowAnnotation()\r
{\r
return this._showAnnotation;\r
- } //-- boolean getShowAnnotation() \r
+ } //-- boolean getShowAnnotation()\r
\r
/**\r
* Returns the value of field 'showBoxes'.\r
- * \r
+ *\r
* @return boolean\r
* @return the value of field 'showBoxes'.\r
*/\r
public boolean getShowBoxes()\r
{\r
return this._showBoxes;\r
- } //-- boolean getShowBoxes() \r
+ } //-- boolean getShowBoxes()\r
\r
/**\r
* Returns the value of field 'showColourText'.\r
- * \r
+ *\r
* @return boolean\r
* @return the value of field 'showColourText'.\r
*/\r
public boolean getShowColourText()\r
{\r
return this._showColourText;\r
- } //-- boolean getShowColourText() \r
+ } //-- boolean getShowColourText()\r
\r
/**\r
* Returns the value of field 'showConservation'.\r
- * \r
+ *\r
* @return boolean\r
* @return the value of field 'showConservation'.\r
*/\r
public boolean getShowConservation()\r
{\r
return this._showConservation;\r
- } //-- boolean getShowConservation() \r
+ } //-- boolean getShowConservation()\r
\r
/**\r
* Returns the value of field 'showFullId'.\r
- * \r
+ *\r
* @return boolean\r
* @return the value of field 'showFullId'.\r
*/\r
public boolean getShowFullId()\r
{\r
return this._showFullId;\r
- } //-- boolean getShowFullId() \r
+ } //-- boolean getShowFullId()\r
\r
/**\r
* Returns the value of field 'showIdentity'.\r
- * \r
+ *\r
* @return boolean\r
* @return the value of field 'showIdentity'.\r
*/\r
public boolean getShowIdentity()\r
{\r
return this._showIdentity;\r
- } //-- boolean getShowIdentity() \r
+ } //-- boolean getShowIdentity()\r
\r
/**\r
* Returns the value of field 'showQuality'.\r
- * \r
+ *\r
* @return boolean\r
* @return the value of field 'showQuality'.\r
*/\r
public boolean getShowQuality()\r
{\r
return this._showQuality;\r
- } //-- boolean getShowQuality() \r
+ } //-- boolean getShowQuality()\r
\r
/**\r
* Returns the value of field 'showSequenceFeatures'.\r
- * \r
+ *\r
* @return boolean\r
* @return the value of field 'showSequenceFeatures'.\r
*/\r
public boolean getShowSequenceFeatures()\r
{\r
return this._showSequenceFeatures;\r
- } //-- boolean getShowSequenceFeatures() \r
+ } //-- boolean getShowSequenceFeatures()\r
\r
/**\r
* Returns the value of field 'showText'.\r
- * \r
+ *\r
* @return boolean\r
* @return the value of field 'showText'.\r
*/\r
public boolean getShowText()\r
{\r
return this._showText;\r
- } //-- boolean getShowText() \r
+ } //-- boolean getShowText()\r
\r
/**\r
* Returns the value of field 'startRes'.\r
- * \r
+ *\r
* @return int\r
* @return the value of field 'startRes'.\r
*/\r
public int getStartRes()\r
{\r
return this._startRes;\r
- } //-- int getStartRes() \r
+ } //-- int getStartRes()\r
\r
/**\r
* Returns the value of field 'startSeq'.\r
- * \r
+ *\r
* @return int\r
* @return the value of field 'startSeq'.\r
*/\r
public int getStartSeq()\r
{\r
return this._startSeq;\r
- } //-- int getStartSeq() \r
+ } //-- int getStartSeq()\r
\r
/**\r
* Returns the value of field 'title'.\r
- * \r
+ *\r
* @return String\r
* @return the value of field 'title'.\r
*/\r
public java.lang.String getTitle()\r
{\r
return this._title;\r
- } //-- java.lang.String getTitle() \r
+ } //-- java.lang.String getTitle()\r
\r
/**\r
* Returns the value of field 'width'.\r
- * \r
+ *\r
* @return int\r
* @return the value of field 'width'.\r
*/\r
public int getWidth()\r
{\r
return this._width;\r
- } //-- int getWidth() \r
+ } //-- int getWidth()\r
\r
/**\r
* Returns the value of field 'wrapAlignment'.\r
- * \r
+ *\r
* @return boolean\r
* @return the value of field 'wrapAlignment'.\r
*/\r
public boolean getWrapAlignment()\r
{\r
return this._wrapAlignment;\r
- } //-- boolean getWrapAlignment() \r
+ } //-- boolean getWrapAlignment()\r
\r
/**\r
* Returns the value of field 'xpos'.\r
- * \r
+ *\r
* @return int\r
* @return the value of field 'xpos'.\r
*/\r
public int getXpos()\r
{\r
return this._xpos;\r
- } //-- int getXpos() \r
+ } //-- int getXpos()\r
\r
/**\r
* Returns the value of field 'ypos'.\r
- * \r
+ *\r
* @return int\r
* @return the value of field 'ypos'.\r
*/\r
public int getYpos()\r
{\r
return this._ypos;\r
- } //-- int getYpos() \r
+ } //-- int getYpos()\r
\r
/**\r
* Method hasConsThreshold\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasConsThreshold()\r
{\r
return this._has_consThreshold;\r
- } //-- boolean hasConsThreshold() \r
+ } //-- boolean hasConsThreshold()\r
\r
/**\r
* Method hasConservationSelected\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasConservationSelected()\r
{\r
return this._has_conservationSelected;\r
- } //-- boolean hasConservationSelected() \r
+ } //-- boolean hasConservationSelected()\r
\r
/**\r
* Method hasFontSize\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasFontSize()\r
{\r
return this._has_fontSize;\r
- } //-- boolean hasFontSize() \r
+ } //-- boolean hasFontSize()\r
\r
/**\r
* Method hasFontStyle\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasFontStyle()\r
{\r
return this._has_fontStyle;\r
- } //-- boolean hasFontStyle() \r
+ } //-- boolean hasFontStyle()\r
\r
/**\r
* Method hasHeight\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasHeight()\r
{\r
return this._has_height;\r
- } //-- boolean hasHeight() \r
+ } //-- boolean hasHeight()\r
\r
/**\r
* Method hasPidSelected\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasPidSelected()\r
{\r
return this._has_pidSelected;\r
- } //-- boolean hasPidSelected() \r
+ } //-- boolean hasPidSelected()\r
\r
/**\r
* Method hasPidThreshold\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasPidThreshold()\r
{\r
return this._has_pidThreshold;\r
- } //-- boolean hasPidThreshold() \r
+ } //-- boolean hasPidThreshold()\r
\r
/**\r
* Method hasRenderGaps\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasRenderGaps()\r
{\r
return this._has_renderGaps;\r
- } //-- boolean hasRenderGaps() \r
+ } //-- boolean hasRenderGaps()\r
\r
/**\r
* Method hasShowAnnotation\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasShowAnnotation()\r
{\r
return this._has_showAnnotation;\r
- } //-- boolean hasShowAnnotation() \r
+ } //-- boolean hasShowAnnotation()\r
\r
/**\r
* Method hasShowBoxes\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasShowBoxes()\r
{\r
return this._has_showBoxes;\r
- } //-- boolean hasShowBoxes() \r
+ } //-- boolean hasShowBoxes()\r
\r
/**\r
* Method hasShowColourText\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasShowColourText()\r
{\r
return this._has_showColourText;\r
- } //-- boolean hasShowColourText() \r
+ } //-- boolean hasShowColourText()\r
\r
/**\r
* Method hasShowConservation\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasShowConservation()\r
{\r
return this._has_showConservation;\r
- } //-- boolean hasShowConservation() \r
+ } //-- boolean hasShowConservation()\r
\r
/**\r
* Method hasShowFullId\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasShowFullId()\r
{\r
return this._has_showFullId;\r
- } //-- boolean hasShowFullId() \r
+ } //-- boolean hasShowFullId()\r
\r
/**\r
* Method hasShowIdentity\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasShowIdentity()\r
{\r
return this._has_showIdentity;\r
- } //-- boolean hasShowIdentity() \r
+ } //-- boolean hasShowIdentity()\r
\r
/**\r
* Method hasShowQuality\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasShowQuality()\r
{\r
return this._has_showQuality;\r
- } //-- boolean hasShowQuality() \r
+ } //-- boolean hasShowQuality()\r
\r
/**\r
* Method hasShowSequenceFeatures\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasShowSequenceFeatures()\r
{\r
return this._has_showSequenceFeatures;\r
- } //-- boolean hasShowSequenceFeatures() \r
+ } //-- boolean hasShowSequenceFeatures()\r
\r
/**\r
* Method hasShowText\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasShowText()\r
{\r
return this._has_showText;\r
- } //-- boolean hasShowText() \r
+ } //-- boolean hasShowText()\r
\r
/**\r
* Method hasStartRes\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasStartRes()\r
{\r
return this._has_startRes;\r
- } //-- boolean hasStartRes() \r
+ } //-- boolean hasStartRes()\r
\r
/**\r
* Method hasStartSeq\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasStartSeq()\r
{\r
return this._has_startSeq;\r
- } //-- boolean hasStartSeq() \r
+ } //-- boolean hasStartSeq()\r
\r
/**\r
* Method hasWidth\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasWidth()\r
{\r
return this._has_width;\r
- } //-- boolean hasWidth() \r
+ } //-- boolean hasWidth()\r
\r
/**\r
* Method hasWrapAlignment\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasWrapAlignment()\r
{\r
return this._has_wrapAlignment;\r
- } //-- boolean hasWrapAlignment() \r
+ } //-- boolean hasWrapAlignment()\r
\r
/**\r
* Method hasXpos\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasXpos()\r
{\r
return this._has_xpos;\r
- } //-- boolean hasXpos() \r
+ } //-- boolean hasXpos()\r
\r
/**\r
* Method hasYpos\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasYpos()\r
{\r
return this._has_ypos;\r
- } //-- boolean hasYpos() \r
+ } //-- boolean hasYpos()\r
\r
/**\r
* Method isValid\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean isValid()\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ } //-- boolean isValid()\r
\r
/**\r
* Method marshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param out\r
*/\r
public void marshal(java.io.Writer out)\r
throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- \r
+\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ } //-- void marshal(java.io.Writer)\r
\r
/**\r
* Method marshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param handler\r
*/\r
public void marshal(org.xml.sax.ContentHandler handler)\r
throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
- \r
+\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ } //-- void marshal(org.xml.sax.ContentHandler)\r
\r
/**\r
* Sets the value of field 'bgColour'.\r
- * \r
+ *\r
* @param bgColour the value of field 'bgColour'.\r
*/\r
public void setBgColour(java.lang.String bgColour)\r
{\r
this._bgColour = bgColour;\r
- } //-- void setBgColour(java.lang.String) \r
+ } //-- void setBgColour(java.lang.String)\r
\r
/**\r
* Sets the value of field 'consThreshold'.\r
- * \r
+ *\r
* @param consThreshold the value of field 'consThreshold'.\r
*/\r
public void setConsThreshold(int consThreshold)\r
{\r
this._consThreshold = consThreshold;\r
this._has_consThreshold = true;\r
- } //-- void setConsThreshold(int) \r
+ } //-- void setConsThreshold(int)\r
\r
/**\r
* Sets the value of field 'conservationSelected'.\r
- * \r
+ *\r
* @param conservationSelected the value of field\r
* 'conservationSelected'.\r
*/\r
{\r
this._conservationSelected = conservationSelected;\r
this._has_conservationSelected = true;\r
- } //-- void setConservationSelected(boolean) \r
+ } //-- void setConservationSelected(boolean)\r
\r
/**\r
* Sets the value of field 'fontName'.\r
- * \r
+ *\r
* @param fontName the value of field 'fontName'.\r
*/\r
public void setFontName(java.lang.String fontName)\r
{\r
this._fontName = fontName;\r
- } //-- void setFontName(java.lang.String) \r
+ } //-- void setFontName(java.lang.String)\r
\r
/**\r
* Sets the value of field 'fontSize'.\r
- * \r
+ *\r
* @param fontSize the value of field 'fontSize'.\r
*/\r
public void setFontSize(int fontSize)\r
{\r
this._fontSize = fontSize;\r
this._has_fontSize = true;\r
- } //-- void setFontSize(int) \r
+ } //-- void setFontSize(int)\r
\r
/**\r
* Sets the value of field 'fontStyle'.\r
- * \r
+ *\r
* @param fontStyle the value of field 'fontStyle'.\r
*/\r
public void setFontStyle(int fontStyle)\r
{\r
this._fontStyle = fontStyle;\r
this._has_fontStyle = true;\r
- } //-- void setFontStyle(int) \r
+ } //-- void setFontStyle(int)\r
\r
/**\r
* Sets the value of field 'height'.\r
- * \r
+ *\r
* @param height the value of field 'height'.\r
*/\r
public void setHeight(int height)\r
{\r
this._height = height;\r
this._has_height = true;\r
- } //-- void setHeight(int) \r
+ } //-- void setHeight(int)\r
\r
/**\r
* Sets the value of field 'pidSelected'.\r
- * \r
+ *\r
* @param pidSelected the value of field 'pidSelected'.\r
*/\r
public void setPidSelected(boolean pidSelected)\r
{\r
this._pidSelected = pidSelected;\r
this._has_pidSelected = true;\r
- } //-- void setPidSelected(boolean) \r
+ } //-- void setPidSelected(boolean)\r
\r
/**\r
* Sets the value of field 'pidThreshold'.\r
- * \r
+ *\r
* @param pidThreshold the value of field 'pidThreshold'.\r
*/\r
public void setPidThreshold(int pidThreshold)\r
{\r
this._pidThreshold = pidThreshold;\r
this._has_pidThreshold = true;\r
- } //-- void setPidThreshold(int) \r
+ } //-- void setPidThreshold(int)\r
\r
/**\r
* Sets the value of field 'renderGaps'.\r
- * \r
+ *\r
* @param renderGaps the value of field 'renderGaps'.\r
*/\r
public void setRenderGaps(boolean renderGaps)\r
{\r
this._renderGaps = renderGaps;\r
this._has_renderGaps = true;\r
- } //-- void setRenderGaps(boolean) \r
+ } //-- void setRenderGaps(boolean)\r
\r
/**\r
* Sets the value of field 'showAnnotation'.\r
- * \r
+ *\r
* @param showAnnotation the value of field 'showAnnotation'.\r
*/\r
public void setShowAnnotation(boolean showAnnotation)\r
{\r
this._showAnnotation = showAnnotation;\r
this._has_showAnnotation = true;\r
- } //-- void setShowAnnotation(boolean) \r
+ } //-- void setShowAnnotation(boolean)\r
\r
/**\r
* Sets the value of field 'showBoxes'.\r
- * \r
+ *\r
* @param showBoxes the value of field 'showBoxes'.\r
*/\r
public void setShowBoxes(boolean showBoxes)\r
{\r
this._showBoxes = showBoxes;\r
this._has_showBoxes = true;\r
- } //-- void setShowBoxes(boolean) \r
+ } //-- void setShowBoxes(boolean)\r
\r
/**\r
* Sets the value of field 'showColourText'.\r
- * \r
+ *\r
* @param showColourText the value of field 'showColourText'.\r
*/\r
public void setShowColourText(boolean showColourText)\r
{\r
this._showColourText = showColourText;\r
this._has_showColourText = true;\r
- } //-- void setShowColourText(boolean) \r
+ } //-- void setShowColourText(boolean)\r
\r
/**\r
* Sets the value of field 'showConservation'.\r
- * \r
+ *\r
* @param showConservation the value of field 'showConservation'\r
*/\r
public void setShowConservation(boolean showConservation)\r
{\r
this._showConservation = showConservation;\r
this._has_showConservation = true;\r
- } //-- void setShowConservation(boolean) \r
+ } //-- void setShowConservation(boolean)\r
\r
/**\r
* Sets the value of field 'showFullId'.\r
- * \r
+ *\r
* @param showFullId the value of field 'showFullId'.\r
*/\r
public void setShowFullId(boolean showFullId)\r
{\r
this._showFullId = showFullId;\r
this._has_showFullId = true;\r
- } //-- void setShowFullId(boolean) \r
+ } //-- void setShowFullId(boolean)\r
\r
/**\r
* Sets the value of field 'showIdentity'.\r
- * \r
+ *\r
* @param showIdentity the value of field 'showIdentity'.\r
*/\r
public void setShowIdentity(boolean showIdentity)\r
{\r
this._showIdentity = showIdentity;\r
this._has_showIdentity = true;\r
- } //-- void setShowIdentity(boolean) \r
+ } //-- void setShowIdentity(boolean)\r
\r
/**\r
* Sets the value of field 'showQuality'.\r
- * \r
+ *\r
* @param showQuality the value of field 'showQuality'.\r
*/\r
public void setShowQuality(boolean showQuality)\r
{\r
this._showQuality = showQuality;\r
this._has_showQuality = true;\r
- } //-- void setShowQuality(boolean) \r
+ } //-- void setShowQuality(boolean)\r
\r
/**\r
* Sets the value of field 'showSequenceFeatures'.\r
- * \r
+ *\r
* @param showSequenceFeatures the value of field\r
* 'showSequenceFeatures'.\r
*/\r
{\r
this._showSequenceFeatures = showSequenceFeatures;\r
this._has_showSequenceFeatures = true;\r
- } //-- void setShowSequenceFeatures(boolean) \r
+ } //-- void setShowSequenceFeatures(boolean)\r
\r
/**\r
* Sets the value of field 'showText'.\r
- * \r
+ *\r
* @param showText the value of field 'showText'.\r
*/\r
public void setShowText(boolean showText)\r
{\r
this._showText = showText;\r
this._has_showText = true;\r
- } //-- void setShowText(boolean) \r
+ } //-- void setShowText(boolean)\r
\r
/**\r
* Sets the value of field 'startRes'.\r
- * \r
+ *\r
* @param startRes the value of field 'startRes'.\r
*/\r
public void setStartRes(int startRes)\r
{\r
this._startRes = startRes;\r
this._has_startRes = true;\r
- } //-- void setStartRes(int) \r
+ } //-- void setStartRes(int)\r
\r
/**\r
* Sets the value of field 'startSeq'.\r
- * \r
+ *\r
* @param startSeq the value of field 'startSeq'.\r
*/\r
public void setStartSeq(int startSeq)\r
{\r
this._startSeq = startSeq;\r
this._has_startSeq = true;\r
- } //-- void setStartSeq(int) \r
+ } //-- void setStartSeq(int)\r
\r
/**\r
* Sets the value of field 'title'.\r
- * \r
+ *\r
* @param title the value of field 'title'.\r
*/\r
public void setTitle(java.lang.String title)\r
{\r
this._title = title;\r
- } //-- void setTitle(java.lang.String) \r
+ } //-- void setTitle(java.lang.String)\r
\r
/**\r
* Sets the value of field 'width'.\r
- * \r
+ *\r
* @param width the value of field 'width'.\r
*/\r
public void setWidth(int width)\r
{\r
this._width = width;\r
this._has_width = true;\r
- } //-- void setWidth(int) \r
+ } //-- void setWidth(int)\r
\r
/**\r
* Sets the value of field 'wrapAlignment'.\r
- * \r
+ *\r
* @param wrapAlignment the value of field 'wrapAlignment'.\r
*/\r
public void setWrapAlignment(boolean wrapAlignment)\r
{\r
this._wrapAlignment = wrapAlignment;\r
this._has_wrapAlignment = true;\r
- } //-- void setWrapAlignment(boolean) \r
+ } //-- void setWrapAlignment(boolean)\r
\r
/**\r
* Sets the value of field 'xpos'.\r
- * \r
+ *\r
* @param xpos the value of field 'xpos'.\r
*/\r
public void setXpos(int xpos)\r
{\r
this._xpos = xpos;\r
this._has_xpos = true;\r
- } //-- void setXpos(int) \r
+ } //-- void setXpos(int)\r
\r
/**\r
* Sets the value of field 'ypos'.\r
- * \r
+ *\r
* @param ypos the value of field 'ypos'.\r
*/\r
public void setYpos(int ypos)\r
{\r
this._ypos = ypos;\r
this._has_ypos = true;\r
- } //-- void setYpos(int) \r
+ } //-- void setYpos(int)\r
\r
/**\r
* Method unmarshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param reader\r
* @return Object\r
*/\r
throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
return (jalview.binding.Viewport) Unmarshaller.unmarshal(jalview.binding.Viewport.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ } //-- java.lang.Object unmarshal(java.io.Reader)\r
\r
/**\r
* Method validate\r
- * \r
+ *\r
*/\r
public void validate()\r
throws org.exolab.castor.xml.ValidationException\r
{\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ } //-- void validate()\r
\r
}\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.datamodel;\r
\r
import jalview.analysis.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.datamodel;\r
\r
public class AlignmentAnnotation\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.datamodel;\r
\r
import java.util.*;\r
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+
package jalview.datamodel;
import java.util.*;
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+
package jalview.datamodel;
import java.awt.*;
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+
package jalview.datamodel;
public class BinaryNode
-/* Jalview - a java multiple alignment editor\r
- * Copyright (C) 1998 Michele Clamp\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., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.\r
- */\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.datamodel;\r
\r
import jalview.io.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.datamodel;\r
\r
import java.util.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.datamodel;\r
\r
import jalview.analysis.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.datamodel;\r
\r
import java.awt.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.datamodel;\r
\r
import jalview.schemes.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.datamodel;\r
\r
import jalview.jbgui.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.datamodel;\r
\r
import java.awt.*;\r
-/* Jalview - a java multiple alignment editor\r
- * Copyright (C) 1998 Michele Clamp\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., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.\r
- */\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
\r
package jalview.datamodel;\r
import java.util.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.datamodel;\r
\r
import jalview.schemes.*;\r
-/********************
- * 2004 Jalview Reengineered
- * Barton Group
- * Dundee University
- *
- * AM Waterhouse
- *******************/
-
-
-
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
package jalview.gui;
public void sortGroupMenuItem_actionPerformed(ActionEvent e)
{
addHistoryItem(new HistoryItem("Group Sort", viewport.alignment, HistoryItem.SORT));
- AlignmentSorter.sortByGroup(viewport.getAlignment());
+ // AlignmentSorter.sortByGroup(viewport.getAlignment());
AlignmentSorter.sortGroups(viewport.getAlignment());
alignPanel.repaint();
}
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.gui;\r
\r
import java.awt.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.gui;\r
\r
import jalview.jbgui.GAlignmentPanel;\r
\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.gui;\r
\r
import javax.swing.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.gui;\r
\r
import jalview.datamodel.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.gui;\r
\r
import java.util.*;\r
-/********************
- * 2004 Jalview Reengineered
- * Barton Group
- * Dundee University
- *
- * AM Waterhouse
- *******************/
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
package jalview.gui;
-/********************\r
- * 2004 Jalview Reengineered\r
- * Barton Group\r
- * Dundee University\r
- *\r
- * AM Waterhouse\r
- *******************/\r
-\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
\r
package jalview.gui;\r
\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.gui;\r
\r
import jalview.datamodel.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.gui;\r
\r
import jalview.jbgui.GFinder;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.gui;\r
\r
import jalview.jbgui.GFontChooser;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.gui;\r
\r
import java.awt.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.gui;\r
\r
import java.awt.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.gui;\r
\r
import javax.swing.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.gui;\r
\r
import java.io.*;\r
import jalview.schemes.*;\r
import javax.swing.JInternalFrame;\r
import java.net.URL;\r
+import jalview.io.SequenceFeatureFetcher;\r
\r
\r
public class Jalview2XML\r
view.getFontStyle(),\r
view.getFontSize()));\r
af.alignPanel.fontChanged();\r
+\r
+ af.sequenceFeatures_actionPerformed(null);\r
af.viewport.setRenderGaps( view.getRenderGaps() );\r
\r
af.viewport.setWrapAlignment( view.getWrapAlignment() );\r
af.changeColour(af.viewport.getGlobalColourScheme());\r
af.viewport.setColourAppliesToAllGroups(true);\r
\r
+ System.out.println(view.getShowSequenceFeatures());\r
+ if( view.getShowSequenceFeatures() );\r
+ {\r
+ SequenceFeatureFetcher sft = new SequenceFeatureFetcher(al, af.alignPanel);\r
+ }\r
\r
//LOAD TREES - THIS RELEASE ONLY ALLOWS 1 TREE\r
if(object.getVamsasModel().getTreeCount()>0)\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.gui;\r
\r
import javax.swing.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.gui;\r
\r
import jalview.datamodel.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.gui;\r
import java.awt.*;\r
import java.util.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.gui;\r
\r
import jalview.datamodel.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.gui;\r
\r
import jalview.datamodel.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.gui;\r
\r
import jalview.jbgui.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.gui;\r
\r
import jalview.jbgui.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.gui;\r
\r
import jalview.math.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.gui;\r
\r
import jalview.datamodel.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.gui;\r
\r
import java.awt.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.gui;\r
\r
import java.awt.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.gui;\r
\r
import jalview.datamodel.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.gui;\r
\r
import jalview.jbgui.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.gui;\r
\r
import javax.swing.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.gui;\r
\r
\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.gui;\r
\r
import jalview.datamodel.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.gui;\r
\r
import jalview.jbgui.GUserDefinedColours;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.gui;\r
\r
import java.awt.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.io;\r
\r
import jalview.datamodel.*;\r
-/* Jalview - a java multiple alignment editor\r
- * Copyright (C) 1998 Michele Clamp\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., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.\r
- */\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.io;\r
\r
import jalview.datamodel.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.io;\r
\r
import jalview.datamodel.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.io;\r
\r
import org.apache.axis.client.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.io;\r
\r
import jalview.datamodel.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.io;\r
\r
import java.io.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.io;\r
\r
import jalview.datamodel.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.io;\r
\r
import jalview.gui.*;\r
-/********************\r
- * 2004 Jalview Reengineered\r
- * Barton Group\r
- * Dundee University\r
- *\r
- * AM Waterhouse\r
- *******************/\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
\r
package jalview.io;\r
\r
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+
/**
* PredFile.java
* JalviewX / Vamsas Project
* JPred.seq.concise reader
*/
+
package jalview.io;
import jalview.datamodel.*;
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
\r
/*///////////////////////////////////////////////////////////////////\r
// This file was taken from java forum\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.io;\r
\r
import javax.swing.filechooser.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.io;\r
\r
import javax.swing.filechooser.FileView;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.io;\r
\r
import jalview.datamodel.*;\r
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+
// NewickFile.java
// Tree I/O
// http://evolution.genetics.washington.edu/phylip/newick_doc.html
+
package jalview.io;
import java.io.*;
-/* Jalview - a java multiple alignment editor\r
- * Copyright (C) 1998 Michele Clamp\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., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.\r
- */\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.io;\r
\r
import jalview.datamodel.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.io;\r
\r
import jalview.datamodel.*;\r
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+
package jalview.io;
/**
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.io;\r
\r
import java.io.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.io;\r
\r
import org.apache.axis.client.*;\r
-/********************\r
- * 2004 Jalview Reengineered\r
- * Barton Group\r
- * Dundee University\r
- *\r
- * AM Waterhouse\r
- *******************/\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
\r
package jalview.jbappletgui;\r
\r
-/********************\r
- * 2004 Jalview Reengineered\r
- * Barton Group\r
- * Dundee University\r
- *\r
- * AM Waterhouse\r
- *******************/\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
\r
package jalview.jbappletgui;\r
\r
-/********************\r
- * 2004 Jalview Reengineered\r
- * Barton Group\r
- * Dundee University\r
- *\r
- * AM Waterhouse\r
- *******************/\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
\r
package jalview.jbappletgui;\r
\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.jbappletgui;\r
\r
import java.awt.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.jbappletgui;\r
\r
import java.awt.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.jbappletgui;\r
\r
import java.awt.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.jbappletgui;\r
\r
import java.awt.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.jbappletgui;\r
\r
import java.awt.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.jbappletgui;\r
\r
import java.awt.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.jbappletgui;\r
\r
import java.awt.*;\r
-/********************\r
- * 2004 Jalview Reengineered\r
- * Barton Group\r
- * Dundee University\r
- *\r
- * AM Waterhouse\r
- *******************/\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
\r
package jalview.jbgui;\r
\r
-/********************
- * 2004 Jalview Reengineered
- * Barton Group
- * Dundee University
- *
- * AM Waterhouse
- *******************/
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
package jalview.jbgui;
-/********************\r
- * 2004 Jalview Reengineered\r
- * Barton Group\r
- * Dundee University\r
- *\r
- * AM Waterhouse\r
- *******************/\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
\r
package jalview.jbgui;\r
\r
-/********************\r
- * 2004 Jalview Reengineered\r
- * Barton Group\r
- * Dundee University\r
- *\r
- * AM Waterhouse\r
- *******************/\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
\r
package jalview.jbgui;\r
\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.jbgui;\r
\r
import javax.swing.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.jbgui;\r
\r
import javax.swing.*;\r
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+
package jalview.jbgui;
import java.awt.*;
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+
package jalview.jbgui;
import javax.swing.*;
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.jbgui;\r
\r
import javax.swing.*;\r
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+
package jalview.jbgui;
import java.awt.*;
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.jbgui;\r
\r
import java.awt.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.jbgui;\r
\r
import javax.swing.*;\r
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+
package jalview.jbgui;
import java.awt.*;
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.math;\r
\r
import jalview.util.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.math;\r
\r
\r
-/* Jalview - a java multiple alignment editor\r
- * Copyright (C) 1998 Michele Clamp\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., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.\r
- */\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
\r
package jalview.schemes;\r
\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.schemes;\r
\r
import java.awt.*;\r
-/* Jalview - a java multiple alignment editor\r
- * Copyright (C) 1998 Michele Clamp\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., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.\r
- */\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
\r
package jalview.schemes;\r
\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.schemes;\r
\r
import java.awt.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.schemes;\r
\r
public class ColourSchemeProperty\r
-/* Jalview - a java multiple alignment editor\r
- * Copyright (C) 1998 Michele Clamp\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., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.\r
- */\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
\r
package jalview.schemes;\r
\r
-/* Jalview - a java multiple alignment editor\r
- * Copyright (C) 1998 Michele Clamp\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., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.\r
- */\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
\r
package jalview.schemes;\r
import java.awt.*;\r
-/* Jalview - a java multiple alignment editor\r
- * Copyright (C) 1998 Michele Clamp\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., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.\r
- */\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
\r
package jalview.schemes;\r
\r
-/* Jalview - a java multiple alignment editor\r
- * Copyright (C) 1998 Michele Clamp\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., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.\r
- */\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
\r
package jalview.schemes;\r
\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.schemes;\r
\r
import java.awt.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.schemes;\r
\r
import jalview.datamodel.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.schemes;\r
\r
import java.util.*;\r
-\r
-/* Copyright (C) 1998 Michele Clamp\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
*\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, 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.\r
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
+\r
package jalview.schemes;\r
\r
import java.awt.Color;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.schemes;\r
\r
import java.awt.*;\r
-\r
-/* Jalview - a java multiple alignment editor\r
- * Copyright (C) 1998 Michele Clamp\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., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.\r
- */\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
\r
package jalview.schemes;\r
\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.schemes;\r
\r
public class TaylorColourScheme extends ResidueColourScheme {\r
-/* Jalview - a java multiple alignment editor\r
- * Copyright (C) 1998 Michele Clamp\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., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.\r
- */\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
\r
package jalview.schemes;\r
\r
-/* Jalview - a java multiple alignment editor\r
- * Copyright (C) 1998 Michele Clamp\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., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.\r
- */\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
\r
package jalview.schemes;\r
\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.schemes;\r
\r
public class ZappoColourScheme extends ResidueColourScheme {\r
-/********************
- * 2004 Jalview Reengineered
- * Barton Group
- * Dundee University
- *
- * AM Waterhouse
- *******************/
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
package jalview.util;
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.util;\r
\r
import jalview.datamodel.*;\r
* @author Cay Horstmann\r
*/\r
\r
+\r
package jalview.util;\r
\r
import java.io.*;\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.util;\r
\r
\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
package jalview.ws;\r
\r
import org.apache.axis.client.*;\r
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+
package jalview.ws;
import org.apache.axis.client.*;
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+
package jalview.ws;
import java.util.Hashtable;
/**
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+
package jalview.ws;
import jalview.gui.WebserviceInfo;
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+
package jalview.ws;
public interface WSClientI
-/* MsaWS.java
- * The basic Multiple Sequence Alignment interface
- * J.B. Procter Feb 2004
- * @header
- */
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
package vamsas;
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
*/
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+
package vamsas.objects.simple;
public class Alignment extends vamsas.objects.simple.Object implements java.io.Serializable {
/**
* Gets the gapchar value for this Alignment.
- *
+ *
* @return gapchar
*/
public java.lang.String getGapchar() {
/**
* Sets the gapchar value for this Alignment.
- *
+ *
* @param gapchar
*/
public void setGapchar(java.lang.String gapchar) {
/**
* Gets the method value for this Alignment.
- *
+ *
* @return method
*/
public java.lang.String[] getMethod() {
/**
* Sets the method value for this Alignment.
- *
+ *
* @param method
*/
public void setMethod(java.lang.String[] method) {
/**
* Gets the seqs value for this Alignment.
- *
+ *
* @return seqs
*/
public vamsas.objects.simple.SequenceSet getSeqs() {
/**
* Sets the seqs value for this Alignment.
- *
+ *
* @param seqs
*/
public void setSeqs(vamsas.objects.simple.SequenceSet seqs) {
}
__equalsCalc = obj;
boolean _equals;
- _equals = super.equals(obj) &&
- ((this.gapchar==null && other.getGapchar()==null) ||
+ _equals = super.equals(obj) &&
+ ((this.gapchar==null && other.getGapchar()==null) ||
(this.gapchar!=null &&
this.gapchar.equals(other.getGapchar()))) &&
- ((this.method==null && other.getMethod()==null) ||
+ ((this.method==null && other.getMethod()==null) ||
(this.method!=null &&
java.util.Arrays.equals(this.method, other.getMethod()))) &&
- ((this.seqs==null && other.getSeqs()==null) ||
+ ((this.seqs==null && other.getSeqs()==null) ||
(this.seqs!=null &&
this.seqs.equals(other.getSeqs())));
__equalsCalc = null;
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
*/
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+
package vamsas.objects.simple;
public class Alignment_Helper {
* Get Custom Serializer
*/
public static org.apache.axis.encoding.Serializer getSerializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
+ java.lang.String mechType,
+ java.lang.Class _javaType,
javax.xml.namespace.QName _xmlType) {
- return
+ return
new org.apache.axis.encoding.ser.BeanSerializer(
_javaType, _xmlType, typeDesc);
}
* Get Custom Deserializer
*/
public static org.apache.axis.encoding.Deserializer getDeserializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
+ java.lang.String mechType,
+ java.lang.Class _javaType,
javax.xml.namespace.QName _xmlType) {
- return
+ return
new org.apache.axis.encoding.ser.BeanDeserializer(
_javaType, _xmlType, typeDesc);
}
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
*/
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+
package vamsas.objects.simple;
public class MsaResult extends vamsas.objects.simple.Result implements java.io.Serializable {
/**
* Gets the msa value for this MsaResult.
- *
+ *
* @return msa
*/
public vamsas.objects.simple.Alignment getMsa() {
/**
* Sets the msa value for this MsaResult.
- *
+ *
* @param msa
*/
public void setMsa(vamsas.objects.simple.Alignment msa) {
}
__equalsCalc = obj;
boolean _equals;
- _equals = super.equals(obj) &&
- ((this.msa==null && other.getMsa()==null) ||
+ _equals = super.equals(obj) &&
+ ((this.msa==null && other.getMsa()==null) ||
(this.msa!=null &&
this.msa.equals(other.getMsa())));
__equalsCalc = null;
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
*/
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+
package vamsas.objects.simple;
public class MsaResult_Helper {
* Get Custom Serializer
*/
public static org.apache.axis.encoding.Serializer getSerializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
+ java.lang.String mechType,
+ java.lang.Class _javaType,
javax.xml.namespace.QName _xmlType) {
- return
+ return
new org.apache.axis.encoding.ser.BeanSerializer(
_javaType, _xmlType, typeDesc);
}
* Get Custom Deserializer
*/
public static org.apache.axis.encoding.Deserializer getDeserializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
+ java.lang.String mechType,
+ java.lang.Class _javaType,
javax.xml.namespace.QName _xmlType) {
- return
+ return
new org.apache.axis.encoding.ser.BeanDeserializer(
_javaType, _xmlType, typeDesc);
}
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
*/
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+
package vamsas.objects.simple;
public abstract class Object implements java.io.Serializable {
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
*/
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+
package vamsas.objects.simple;
public class Object_Helper {
* Get Custom Serializer
*/
public static org.apache.axis.encoding.Serializer getSerializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
+ java.lang.String mechType,
+ java.lang.Class _javaType,
javax.xml.namespace.QName _xmlType) {
- return
+ return
new org.apache.axis.encoding.ser.BeanSerializer(
_javaType, _xmlType, typeDesc);
}
* Get Custom Deserializer
*/
public static org.apache.axis.encoding.Deserializer getDeserializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
+ java.lang.String mechType,
+ java.lang.Class _javaType,
javax.xml.namespace.QName _xmlType) {
- return
+ return
new org.apache.axis.encoding.ser.BeanDeserializer(
_javaType, _xmlType, typeDesc);
}
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
*/
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+
package vamsas.objects.simple;
public class Result implements java.io.Serializable {
/**
* Gets the broken value for this Result.
- *
+ *
* @return broken
*/
public boolean isBroken() {
/**
* Sets the broken value for this Result.
- *
+ *
* @param broken
*/
public void setBroken(boolean broken) {
/**
* Gets the failed value for this Result.
- *
+ *
* @return failed
*/
public boolean isFailed() {
/**
* Sets the failed value for this Result.
- *
+ *
* @param failed
*/
public void setFailed(boolean failed) {
/**
* Gets the finished value for this Result.
- *
+ *
* @return finished
*/
public boolean isFinished() {
/**
* Sets the finished value for this Result.
- *
+ *
* @param finished
*/
public void setFinished(boolean finished) {
/**
* Gets the invalid value for this Result.
- *
+ *
* @return invalid
*/
public boolean isInvalid() {
/**
* Sets the invalid value for this Result.
- *
+ *
* @param invalid
*/
public void setInvalid(boolean invalid) {
/**
* Gets the jobFailed value for this Result.
- *
+ *
* @return jobFailed
*/
public boolean isJobFailed() {
/**
* Sets the jobFailed value for this Result.
- *
+ *
* @param jobFailed
*/
public void setJobFailed(boolean jobFailed) {
/**
* Gets the queued value for this Result.
- *
+ *
* @return queued
*/
public boolean isQueued() {
/**
* Sets the queued value for this Result.
- *
+ *
* @param queued
*/
public void setQueued(boolean queued) {
/**
* Gets the running value for this Result.
- *
+ *
* @return running
*/
public boolean isRunning() {
/**
* Sets the running value for this Result.
- *
+ *
* @param running
*/
public void setRunning(boolean running) {
/**
* Gets the serverError value for this Result.
- *
+ *
* @return serverError
*/
public boolean isServerError() {
/**
* Sets the serverError value for this Result.
- *
+ *
* @param serverError
*/
public void setServerError(boolean serverError) {
/**
* Gets the state value for this Result.
- *
+ *
* @return state
*/
public int getState() {
/**
* Sets the state value for this Result.
- *
+ *
* @param state
*/
public void setState(int state) {
/**
* Gets the status value for this Result.
- *
+ *
* @return status
*/
public java.lang.String getStatus() {
/**
* Sets the status value for this Result.
- *
+ *
* @param status
*/
public void setStatus(java.lang.String status) {
/**
* Gets the suspended value for this Result.
- *
+ *
* @return suspended
*/
public boolean isSuspended() {
/**
* Sets the suspended value for this Result.
- *
+ *
* @param suspended
*/
public void setSuspended(boolean suspended) {
}
__equalsCalc = obj;
boolean _equals;
- _equals = true &&
+ _equals = true &&
this.broken == other.isBroken() &&
this.failed == other.isFailed() &&
this.finished == other.isFinished() &&
this.running == other.isRunning() &&
this.serverError == other.isServerError() &&
this.state == other.getState() &&
- ((this.status==null && other.getStatus()==null) ||
+ ((this.status==null && other.getStatus()==null) ||
(this.status!=null &&
this.status.equals(other.getStatus()))) &&
this.suspended == other.isSuspended();
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
*/
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+
package vamsas.objects.simple;
public class Result_Helper {
* Get Custom Serializer
*/
public static org.apache.axis.encoding.Serializer getSerializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
+ java.lang.String mechType,
+ java.lang.Class _javaType,
javax.xml.namespace.QName _xmlType) {
- return
+ return
new org.apache.axis.encoding.ser.BeanSerializer(
_javaType, _xmlType, typeDesc);
}
* Get Custom Deserializer
*/
public static org.apache.axis.encoding.Deserializer getDeserializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
+ java.lang.String mechType,
+ java.lang.Class _javaType,
javax.xml.namespace.QName _xmlType) {
- return
+ return
new org.apache.axis.encoding.ser.BeanDeserializer(
_javaType, _xmlType, typeDesc);
}
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
*/
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+
package vamsas.objects.simple;
public class Sequence implements java.io.Serializable {
/**
* Gets the id value for this Sequence.
- *
+ *
* @return id
*/
public java.lang.String getId() {
/**
* Sets the id value for this Sequence.
- *
+ *
* @param id
*/
public void setId(java.lang.String id) {
/**
* Gets the seq value for this Sequence.
- *
+ *
* @return seq
*/
public java.lang.String getSeq() {
/**
* Sets the seq value for this Sequence.
- *
+ *
* @param seq
*/
public void setSeq(java.lang.String seq) {
}
__equalsCalc = obj;
boolean _equals;
- _equals = true &&
- ((this.id==null && other.getId()==null) ||
+ _equals = true &&
+ ((this.id==null && other.getId()==null) ||
(this.id!=null &&
this.id.equals(other.getId()))) &&
- ((this.seq==null && other.getSeq()==null) ||
+ ((this.seq==null && other.getSeq()==null) ||
(this.seq!=null &&
this.seq.equals(other.getSeq())));
__equalsCalc = null;
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
*/
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+
package vamsas.objects.simple;
public class SequenceSet implements java.io.Serializable {
/**
* Gets the seqs value for this SequenceSet.
- *
+ *
* @return seqs
*/
public vamsas.objects.simple.Sequence[] getSeqs() {
/**
* Sets the seqs value for this SequenceSet.
- *
+ *
* @param seqs
*/
public void setSeqs(vamsas.objects.simple.Sequence[] seqs) {
}
__equalsCalc = obj;
boolean _equals;
- _equals = true &&
- ((this.seqs==null && other.getSeqs()==null) ||
+ _equals = true &&
+ ((this.seqs==null && other.getSeqs()==null) ||
(this.seqs!=null &&
java.util.Arrays.equals(this.seqs, other.getSeqs())));
__equalsCalc = null;
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
*/
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+
package vamsas.objects.simple;
public class SequenceSet_Helper {
* Get Custom Serializer
*/
public static org.apache.axis.encoding.Serializer getSerializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
+ java.lang.String mechType,
+ java.lang.Class _javaType,
javax.xml.namespace.QName _xmlType) {
- return
+ return
new org.apache.axis.encoding.ser.BeanSerializer(
_javaType, _xmlType, typeDesc);
}
* Get Custom Deserializer
*/
public static org.apache.axis.encoding.Deserializer getDeserializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
+ java.lang.String mechType,
+ java.lang.Class _javaType,
javax.xml.namespace.QName _xmlType) {
- return
+ return
new org.apache.axis.encoding.ser.BeanDeserializer(
_javaType, _xmlType, typeDesc);
}
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
*/
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+
package vamsas.objects.simple;
public class Sequence_Helper {
* Get Custom Serializer
*/
public static org.apache.axis.encoding.Serializer getSerializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
+ java.lang.String mechType,
+ java.lang.Class _javaType,
javax.xml.namespace.QName _xmlType) {
- return
+ return
new org.apache.axis.encoding.ser.BeanSerializer(
_javaType, _xmlType, typeDesc);
}
* Get Custom Deserializer
*/
public static org.apache.axis.encoding.Deserializer getDeserializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
+ java.lang.String mechType,
+ java.lang.Class _javaType,
javax.xml.namespace.QName _xmlType) {
- return
+ return
new org.apache.axis.encoding.ser.BeanDeserializer(
_javaType, _xmlType, typeDesc);
}
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
*/
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+
package vamsas.objects.simple;
public class WsJobId implements java.io.Serializable {
/**
* Gets the jobId value for this WsJobId.
- *
+ *
* @return jobId
*/
public java.lang.String getJobId() {
/**
* Sets the jobId value for this WsJobId.
- *
+ *
* @param jobId
*/
public void setJobId(java.lang.String jobId) {
/**
* Gets the status value for this WsJobId.
- *
+ *
* @return status
*/
public int getStatus() {
/**
* Sets the status value for this WsJobId.
- *
+ *
* @param status
*/
public void setStatus(int status) {
}
__equalsCalc = obj;
boolean _equals;
- _equals = true &&
- ((this.jobId==null && other.getJobId()==null) ||
+ _equals = true &&
+ ((this.jobId==null && other.getJobId()==null) ||
(this.jobId!=null &&
this.jobId.equals(other.getJobId()))) &&
this.status == other.getStatus();
* by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
*/
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+
package vamsas.objects.simple;
public class WsJobId_Helper {
* Get Custom Serializer
*/
public static org.apache.axis.encoding.Serializer getSerializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
+ java.lang.String mechType,
+ java.lang.Class _javaType,
javax.xml.namespace.QName _xmlType) {
- return
+ return
new org.apache.axis.encoding.ser.BeanSerializer(
_javaType, _xmlType, typeDesc);
}
* Get Custom Deserializer
*/
public static org.apache.axis.encoding.Deserializer getDeserializer(
- java.lang.String mechType,
- java.lang.Class _javaType,
+ java.lang.String mechType,
+ java.lang.Class _javaType,
javax.xml.namespace.QName _xmlType) {
- return
+ return
new org.apache.axis.encoding.ser.BeanDeserializer(
_javaType, _xmlType, typeDesc);
}
git://source.jalview.org / jalview.git / commitdiff