X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FJGroup.java;h=555c2fdb7d132d35c3a6c245907bdf2b00b4cd34;hb=680885310ca5bca2a9b1bfd1c2dd79147d6f4b8d;hp=a0117ee7529ca8b5e3e8dceb846be8590fdc0707;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/binding/JGroup.java b/src/jalview/binding/JGroup.java old mode 100755 new mode 100644 index a0117ee..555c2fd --- a/src/jalview/binding/JGroup.java +++ b/src/jalview/binding/JGroup.java @@ -1,26 +1,15 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 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 + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.binding; -// ---------------------------------/ -// - Imported classes and packages -/ -// ---------------------------------/ +//---------------------------------/ +//- Imported classes and packages -/ +//---------------------------------/ import org.exolab.castor.xml.Marshaller; import org.exolab.castor.xml.Unmarshaller; @@ -151,7 +140,7 @@ public class JGroup implements java.io.Serializable * * @param vSeq * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection + * if the index given is outside the bounds of the collection */ public void addSeq(final int vSeq) throws java.lang.IndexOutOfBoundsException @@ -165,7 +154,7 @@ public class JGroup implements java.io.Serializable * @param index * @param vSeq * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection + * if the index given is outside the bounds of the collection */ public void addSeq(final int index, final int vSeq) throws java.lang.IndexOutOfBoundsException @@ -174,56 +163,56 @@ public class JGroup implements java.io.Serializable } /** - */ + */ public void deleteColourText() { this._has_colourText = false; } /** - */ + */ public void deleteConsThreshold() { this._has_consThreshold = false; } /** - */ + */ public void deleteDisplayBoxes() { this._has_displayBoxes = false; } /** - */ + */ public void deleteDisplayText() { this._has_displayText = false; } /** - */ + */ public void deleteEnd() { this._has_end = false; } /** - */ + */ public void deleteOutlineColour() { this._has_outlineColour = false; } /** - */ + */ public void deletePidThreshold() { this._has_pidThreshold = false; } /** - */ + */ public void deleteStart() { this._has_start = false; @@ -334,7 +323,7 @@ public class JGroup implements java.io.Serializable * * @param index * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection + * if the index given is outside the bounds of the collection * @return the value of the int at the given index */ public int getSeq(final int index) @@ -519,11 +508,10 @@ public class JGroup implements java.io.Serializable * * @param out * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling + * if object is null or if any SAXException is thrown during + * marshaling * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the - * schema + * if this object is an invalid instance according to the schema */ public void marshal(final java.io.Writer out) throws org.exolab.castor.xml.MarshalException, @@ -537,13 +525,12 @@ public class JGroup implements java.io.Serializable * * @param handler * @throws java.io.IOException - * if an IOException occurs during marshaling + * if an IOException occurs during marshaling * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the - * schema + * if this object is an invalid instance according to the schema * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling + * if object is null or if any SAXException is thrown during + * marshaling */ public void marshal(final org.xml.sax.ContentHandler handler) throws java.io.IOException, @@ -554,7 +541,7 @@ public class JGroup implements java.io.Serializable } /** - */ + */ public void removeAllSeq() { this._seqList.clear(); @@ -588,7 +575,7 @@ public class JGroup implements java.io.Serializable * Sets the value of field 'colour'. * * @param colour - * the value of field 'colour'. + * the value of field 'colour'. */ public void setColour(final java.lang.String colour) { @@ -599,7 +586,7 @@ public class JGroup implements java.io.Serializable * Sets the value of field 'colourText'. * * @param colourText - * the value of field 'colourText'. + * the value of field 'colourText'. */ public void setColourText(final boolean colourText) { @@ -611,7 +598,7 @@ public class JGroup implements java.io.Serializable * Sets the value of field 'consThreshold'. * * @param consThreshold - * the value of field 'consThreshold'. + * the value of field 'consThreshold'. */ public void setConsThreshold(final int consThreshold) { @@ -623,7 +610,7 @@ public class JGroup implements java.io.Serializable * Sets the value of field 'displayBoxes'. * * @param displayBoxes - * the value of field 'displayBoxes'. + * the value of field 'displayBoxes'. */ public void setDisplayBoxes(final boolean displayBoxes) { @@ -635,7 +622,7 @@ public class JGroup implements java.io.Serializable * Sets the value of field 'displayText'. * * @param displayText - * the value of field 'displayText'. + * the value of field 'displayText'. */ public void setDisplayText(final boolean displayText) { @@ -647,7 +634,7 @@ public class JGroup implements java.io.Serializable * Sets the value of field 'end'. * * @param end - * the value of field 'end'. + * the value of field 'end'. */ public void setEnd(final int end) { @@ -659,7 +646,7 @@ public class JGroup implements java.io.Serializable * Sets the value of field 'name'. * * @param name - * the value of field 'name'. + * the value of field 'name'. */ public void setName(final java.lang.String name) { @@ -670,7 +657,7 @@ public class JGroup implements java.io.Serializable * Sets the value of field 'outlineColour'. * * @param outlineColour - * the value of field 'outlineColour'. + * the value of field 'outlineColour'. */ public void setOutlineColour(final int outlineColour) { @@ -682,7 +669,7 @@ public class JGroup implements java.io.Serializable * Sets the value of field 'pidThreshold'. * * @param pidThreshold - * the value of field 'pidThreshold'. + * the value of field 'pidThreshold'. */ public void setPidThreshold(final int pidThreshold) { @@ -696,7 +683,7 @@ public class JGroup implements java.io.Serializable * @param index * @param vSeq * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection + * if the index given is outside the bounds of the collection */ public void setSeq(final int index, final int vSeq) throws java.lang.IndexOutOfBoundsException @@ -731,7 +718,7 @@ public class JGroup implements java.io.Serializable * Sets the value of field 'start'. * * @param start - * the value of field 'start'. + * the value of field 'start'. */ public void setStart(final int start) { @@ -744,27 +731,26 @@ public class JGroup implements java.io.Serializable * * @param reader * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling + * if object is null or if any SAXException is thrown during + * marshaling * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the - * schema + * if this object is an invalid instance according to the schema * @return the unmarshaled jalview.binding.JGroup */ - public static jalview.binding.JGroup unmarshal(final java.io.Reader reader) + public static jalview.binding.JGroup unmarshal( + final java.io.Reader reader) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.binding.JGroup) Unmarshaller.unmarshal( - jalview.binding.JGroup.class, reader); + return (jalview.binding.JGroup) Unmarshaller + .unmarshal(jalview.binding.JGroup.class, reader); } /** * * * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the - * schema + * if this object is an invalid instance according to the schema */ public void validate() throws org.exolab.castor.xml.ValidationException {