X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FJGroup.java;h=4da0f75f76ed3f64cf6def9c2327192bd10cf919;hb=95114daeda16764e98a2d8eb0b47acbeeeba5bcf;hp=c24533e7288776264a9cf68f3252c620ba818d6c;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/schemabinding/version2/JGroup.java b/src/jalview/schemabinding/version2/JGroup.java index c24533e..4da0f75 100755 --- a/src/jalview/schemabinding/version2/JGroup.java +++ b/src/jalview/schemabinding/version2/JGroup.java @@ -1,26 +1,25 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) + * Copyright (C) 2010 J Procter, AM Waterhouse, 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 file is part of Jalview. * - * 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. + * Jalview 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 3 of the License, or (at your option) any later version. * - * 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 + * Jalview 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 Jalview. If not, see . */ package jalview.schemabinding.version2; -// ---------------------------------/ -// - Imported classes and packages -/ -// ---------------------------------/ +//---------------------------------/ +//- Imported classes and packages -/ +//---------------------------------/ import org.exolab.castor.xml.Marshaller; import org.exolab.castor.xml.Unmarshaller; @@ -158,6 +157,52 @@ public class JGroup implements java.io.Serializable private boolean _has_textColThreshold; /** + * Field _showUnconserved. + */ + private boolean _showUnconserved; + + /** + * keeps track of state for field: _showUnconserved + */ + private boolean _has_showUnconserved; + + /** + * Field _ignoreGapsinConsensus. + */ + private boolean _ignoreGapsinConsensus = true; + + /** + * keeps track of state for field: _ignoreGapsinConsensus + */ + private boolean _has_ignoreGapsinConsensus; + + /** + * Field _showConsensusHistogram. + */ + private boolean _showConsensusHistogram = true; + + /** + * keeps track of state for field: _showConsensusHistogram + */ + private boolean _has_showConsensusHistogram; + + /** + * Field _showSequenceLogo. + */ + private boolean _showSequenceLogo = false; + + /** + * keeps track of state for field: _showSequenceLogo + */ + private boolean _has_showSequenceLogo; + + /** + * Optional sequence group ID (only needs to be unique for this alignment) + * + */ + private java.lang.String _id; + + /** * Field _seqList. */ private java.util.Vector _seqList; @@ -181,7 +226,7 @@ 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 java.lang.String vSeq) throws java.lang.IndexOutOfBoundsException @@ -195,7 +240,7 @@ 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 java.lang.String vSeq) throws java.lang.IndexOutOfBoundsException @@ -204,77 +249,105 @@ 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 deleteIgnoreGapsinConsensus() + { + this._has_ignoreGapsinConsensus = false; + } + + /** + */ public void deleteOutlineColour() { this._has_outlineColour = false; } /** - */ + */ public void deletePidThreshold() { this._has_pidThreshold = false; } /** - */ + */ + public void deleteShowConsensusHistogram() + { + this._has_showConsensusHistogram = false; + } + + /** + */ + public void deleteShowSequenceLogo() + { + this._has_showSequenceLogo = false; + } + + /** + */ + public void deleteShowUnconserved() + { + this._has_showUnconserved = false; + } + + /** + */ public void deleteStart() { this._has_start = false; } /** - */ + */ public void deleteTextCol1() { this._has_textCol1 = false; } /** - */ + */ public void deleteTextCol2() { this._has_textCol2 = false; } /** - */ + */ public void deleteTextColThreshold() { this._has_textColThreshold = false; @@ -351,6 +424,29 @@ public class JGroup implements java.io.Serializable } /** + * Returns the value of field 'id'. The field 'id' has the following + * description: Optional sequence group ID (only needs to be unique for this + * alignment) + * + * + * @return the value of field 'Id'. + */ + public java.lang.String getId() + { + return this._id; + } + + /** + * Returns the value of field 'ignoreGapsinConsensus'. + * + * @return the value of field 'IgnoreGapsinConsensus'. + */ + public boolean getIgnoreGapsinConsensus() + { + return this._ignoreGapsinConsensus; + } + + /** * Returns the value of field 'name'. * * @return the value of field 'Name'. @@ -385,7 +481,7 @@ 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 java.lang.String at the given index */ public java.lang.String getSeq(final int index) @@ -427,6 +523,36 @@ public class JGroup implements java.io.Serializable } /** + * Returns the value of field 'showConsensusHistogram'. + * + * @return the value of field 'ShowConsensusHistogram'. + */ + public boolean getShowConsensusHistogram() + { + return this._showConsensusHistogram; + } + + /** + * Returns the value of field 'showSequenceLogo'. + * + * @return the value of field 'ShowSequenceLogo'. + */ + public boolean getShowSequenceLogo() + { + return this._showSequenceLogo; + } + + /** + * Returns the value of field 'showUnconserved'. + * + * @return the value of field 'ShowUnconserved'. + */ + public boolean getShowUnconserved() + { + return this._showUnconserved; + } + + /** * Returns the value of field 'start'. * * @return the value of field 'Start'. @@ -517,6 +643,16 @@ public class JGroup implements java.io.Serializable } /** + * Method hasIgnoreGapsinConsensus. + * + * @return true if at least one IgnoreGapsinConsensus has been added + */ + public boolean hasIgnoreGapsinConsensus() + { + return this._has_ignoreGapsinConsensus; + } + + /** * Method hasOutlineColour. * * @return true if at least one OutlineColour has been added @@ -537,6 +673,36 @@ public class JGroup implements java.io.Serializable } /** + * Method hasShowConsensusHistogram. + * + * @return true if at least one ShowConsensusHistogram has been added + */ + public boolean hasShowConsensusHistogram() + { + return this._has_showConsensusHistogram; + } + + /** + * Method hasShowSequenceLogo. + * + * @return true if at least one ShowSequenceLogo has been added + */ + public boolean hasShowSequenceLogo() + { + return this._has_showSequenceLogo; + } + + /** + * Method hasShowUnconserved. + * + * @return true if at least one ShowUnconserved has been added + */ + public boolean hasShowUnconserved() + { + return this._has_showUnconserved; + } + + /** * Method hasStart. * * @return true if at least one Start has been added @@ -607,6 +773,46 @@ public class JGroup implements java.io.Serializable } /** + * Returns the value of field 'ignoreGapsinConsensus'. + * + * @return the value of field 'IgnoreGapsinConsensus'. + */ + public boolean isIgnoreGapsinConsensus() + { + return this._ignoreGapsinConsensus; + } + + /** + * Returns the value of field 'showConsensusHistogram'. + * + * @return the value of field 'ShowConsensusHistogram'. + */ + public boolean isShowConsensusHistogram() + { + return this._showConsensusHistogram; + } + + /** + * Returns the value of field 'showSequenceLogo'. + * + * @return the value of field 'ShowSequenceLogo'. + */ + public boolean isShowSequenceLogo() + { + return this._showSequenceLogo; + } + + /** + * Returns the value of field 'showUnconserved'. + * + * @return the value of field 'ShowUnconserved'. + */ + public boolean isShowUnconserved() + { + return this._showUnconserved; + } + + /** * Method isValid. * * @return true if this object is valid according to the schema @@ -628,11 +834,10 @@ 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, @@ -646,13 +851,12 @@ 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, @@ -663,7 +867,7 @@ public class JGroup implements java.io.Serializable } /** - */ + */ public void removeAllSeq() { this._seqList.clear(); @@ -697,7 +901,7 @@ 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) { @@ -708,7 +912,7 @@ 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) { @@ -720,7 +924,7 @@ 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) { @@ -732,7 +936,7 @@ 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) { @@ -744,7 +948,7 @@ 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) { @@ -756,7 +960,7 @@ 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) { @@ -765,10 +969,35 @@ public class JGroup implements java.io.Serializable } /** + * Sets the value of field 'id'. The field 'id' has the following description: + * Optional sequence group ID (only needs to be unique for this alignment) + * + * + * @param id + * the value of field 'id'. + */ + public void setId(final java.lang.String id) + { + this._id = id; + } + + /** + * Sets the value of field 'ignoreGapsinConsensus'. + * + * @param ignoreGapsinConsensus + * the value of field 'ignoreGapsinConsensus'. + */ + public void setIgnoreGapsinConsensus(final boolean ignoreGapsinConsensus) + { + this._ignoreGapsinConsensus = ignoreGapsinConsensus; + this._has_ignoreGapsinConsensus = true; + } + + /** * 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) { @@ -779,7 +1008,7 @@ 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) { @@ -791,7 +1020,7 @@ 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) { @@ -805,7 +1034,7 @@ 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 java.lang.String vSeq) throws java.lang.IndexOutOfBoundsException @@ -837,10 +1066,46 @@ public class JGroup implements java.io.Serializable } /** + * Sets the value of field 'showConsensusHistogram'. + * + * @param showConsensusHistogram + * the value of field 'showConsensusHistogram'. + */ + public void setShowConsensusHistogram(final boolean showConsensusHistogram) + { + this._showConsensusHistogram = showConsensusHistogram; + this._has_showConsensusHistogram = true; + } + + /** + * Sets the value of field 'showSequenceLogo'. + * + * @param showSequenceLogo + * the value of field 'showSequenceLogo' + */ + public void setShowSequenceLogo(final boolean showSequenceLogo) + { + this._showSequenceLogo = showSequenceLogo; + this._has_showSequenceLogo = true; + } + + /** + * Sets the value of field 'showUnconserved'. + * + * @param showUnconserved + * the value of field 'showUnconserved'. + */ + public void setShowUnconserved(final boolean showUnconserved) + { + this._showUnconserved = showUnconserved; + this._has_showUnconserved = true; + } + + /** * Sets the value of field 'start'. * * @param start - * the value of field 'start'. + * the value of field 'start'. */ public void setStart(final int start) { @@ -852,7 +1117,7 @@ public class JGroup implements java.io.Serializable * Sets the value of field 'textCol1'. * * @param textCol1 - * the value of field 'textCol1'. + * the value of field 'textCol1'. */ public void setTextCol1(final int textCol1) { @@ -864,7 +1129,7 @@ public class JGroup implements java.io.Serializable * Sets the value of field 'textCol2'. * * @param textCol2 - * the value of field 'textCol2'. + * the value of field 'textCol2'. */ public void setTextCol2(final int textCol2) { @@ -876,7 +1141,7 @@ public class JGroup implements java.io.Serializable * Sets the value of field 'textColThreshold'. * * @param textColThreshold - * the value of field 'textColThreshold' + * the value of field 'textColThreshold' */ public void setTextColThreshold(final int textColThreshold) { @@ -889,11 +1154,10 @@ 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.schemabinding.version2.JGroup */ public static jalview.schemabinding.version2.JGroup unmarshal( @@ -909,8 +1173,7 @@ public class JGroup implements java.io.Serializable * * * @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 {