X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FViewport.java;h=7dcb3eeac28b447d9e982056abddce8fe45e3f33;hb=ff2d6b48be7f17742defac9c965c70d7944d773b;hp=948d7d0da5aeaa4dd1caae7fcbdda928600f9fd9;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git diff --git a/src/jalview/schemabinding/version2/Viewport.java b/src/jalview/schemabinding/version2/Viewport.java index 948d7d0..7dcb3ee 100644 --- a/src/jalview/schemabinding/version2/Viewport.java +++ b/src/jalview/schemabinding/version2/Viewport.java @@ -1,20 +1,3 @@ -/******************************************************************************* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) - * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * 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. - * - * 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 . - *******************************************************************************/ /* * This class was automatically generated with * Castor 1.1, using an XML @@ -284,6 +267,16 @@ public class Viewport implements java.io.Serializable { private boolean _has_showSequenceLogo; /** + * Field _normaliseSequenceLogo. + */ + private boolean _normaliseSequenceLogo = false; + + /** + * keeps track of state for field: _normaliseSequenceLogo + */ + private boolean _has_normaliseSequenceLogo; + + /** * Field _ignoreGapsinConsensus. */ private boolean _ignoreGapsinConsensus = true; @@ -389,13 +382,21 @@ public class Viewport implements java.io.Serializable { private boolean _has_textColThreshold; /** - * unique id used by jalview to synchronize between stored and - * instantiated views + * unique id used by jalview to + * synchronize between stored and + * instantiated views * */ private java.lang.String _id; /** + * The viewport id of this viewport's (cdna/protein) coding + * complement, if any + * + */ + private java.lang.String _complementId; + + /** * Field _width. */ private int _width; @@ -445,6 +446,11 @@ public class Viewport implements java.io.Serializable { */ private java.util.Vector _hiddenColumnsList; + /** + * Field _calcIdParamList. + */ + private java.util.Vector _calcIdParamList; + //----------------/ //- Constructors -/ @@ -453,6 +459,7 @@ public class Viewport implements java.io.Serializable { public Viewport() { super(); this._hiddenColumnsList = new java.util.Vector(); + this._calcIdParamList = new java.util.Vector(); } @@ -463,6 +470,34 @@ public class Viewport implements java.io.Serializable { /** * * + * @param vCalcIdParam + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addCalcIdParam( + final jalview.schemabinding.version2.CalcIdParam vCalcIdParam) + throws java.lang.IndexOutOfBoundsException { + this._calcIdParamList.addElement(vCalcIdParam); + } + + /** + * + * + * @param index + * @param vCalcIdParam + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addCalcIdParam( + final int index, + final jalview.schemabinding.version2.CalcIdParam vCalcIdParam) + throws java.lang.IndexOutOfBoundsException { + this._calcIdParamList.add(index, vCalcIdParam); + } + + /** + * + * * @param vHiddenColumns * @throws java.lang.IndexOutOfBoundsException if the index * given is outside the bounds of the collection @@ -560,6 +595,13 @@ public class Viewport implements java.io.Serializable { /** */ + public void deleteNormaliseSequenceLogo( + ) { + this._has_normaliseSequenceLogo= false; + } + + /** + */ public void deletePidSelected( ) { this._has_pidSelected= false; @@ -741,6 +783,17 @@ public class Viewport implements java.io.Serializable { } /** + * Method enumerateCalcIdParam. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.CalcIdParam elements + */ + public java.util.Enumeration enumerateCalcIdParam( + ) { + return this._calcIdParamList.elements(); + } + + /** * Method enumerateHiddenColumns. * * @return an Enumeration over all @@ -772,6 +825,51 @@ public class Viewport implements java.io.Serializable { } /** + * Method getCalcIdParam. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the + * jalview.schemabinding.version2.CalcIdParam at the given index + */ + public jalview.schemabinding.version2.CalcIdParam getCalcIdParam( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._calcIdParamList.size()) { + throw new IndexOutOfBoundsException("getCalcIdParam: Index value '" + index + "' not in range [0.." + (this._calcIdParamList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.CalcIdParam) _calcIdParamList.get(index); + } + + /** + * Method getCalcIdParam.Returns the contents of the collection + * in an Array.

Note: Just in case the collection contents + * are changing in another thread, we pass a 0-length Array of + * the correct type into the API call. This way we know + * that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public jalview.schemabinding.version2.CalcIdParam[] getCalcIdParam( + ) { + jalview.schemabinding.version2.CalcIdParam[] array = new jalview.schemabinding.version2.CalcIdParam[0]; + return (jalview.schemabinding.version2.CalcIdParam[]) this._calcIdParamList.toArray(array); + } + + /** + * Method getCalcIdParamCount. + * + * @return the size of this collection + */ + public int getCalcIdParamCount( + ) { + return this._calcIdParamList.size(); + } + + /** * Returns the value of field 'centreColumnLabels'. * * @return the value of field 'CentreColumnLabels'. @@ -782,6 +880,20 @@ public class Viewport implements java.io.Serializable { } /** + * Returns the value of field 'complementId'. The field + * 'complementId' has the following description: The viewport + * id of this viewport's (cdna/protein) coding complement, if + * any + * + * + * @return the value of field 'ComplementId'. + */ + public java.lang.String getComplementId( + ) { + return this._complementId; + } + + /** * Returns the value of field 'consThreshold'. * * @return the value of field 'ConsThreshold'. @@ -921,7 +1033,8 @@ public class Viewport implements java.io.Serializable { /** * Returns the value of field 'id'. The field 'id' has the * following description: unique id used by jalview to - * synchronize between stored and instantiated views + * synchronize between stored and + * instantiated views * * * @return the value of field 'Id'. @@ -942,6 +1055,16 @@ public class Viewport implements java.io.Serializable { } /** + * Returns the value of field 'normaliseSequenceLogo'. + * + * @return the value of field 'NormaliseSequenceLogo'. + */ + public boolean getNormaliseSequenceLogo( + ) { + return this._normaliseSequenceLogo; + } + + /** * Returns the value of field 'pidSelected'. * * @return the value of field 'PidSelected'. @@ -1334,6 +1457,17 @@ public class Viewport implements java.io.Serializable { } /** + * Method hasNormaliseSequenceLogo. + * + * @return true if at least one NormaliseSequenceLogo has been + * added + */ + public boolean hasNormaliseSequenceLogo( + ) { + return this._has_normaliseSequenceLogo; + } + + /** * Method hasPidSelected. * * @return true if at least one PidSelected has been added @@ -1658,6 +1792,16 @@ public class Viewport implements java.io.Serializable { } /** + * Returns the value of field 'normaliseSequenceLogo'. + * + * @return the value of field 'NormaliseSequenceLogo'. + */ + public boolean isNormaliseSequenceLogo( + ) { + return this._normaliseSequenceLogo; + } + + /** * Returns the value of field 'pidSelected'. * * @return the value of field 'PidSelected'. @@ -1876,12 +2020,43 @@ public class Viewport implements java.io.Serializable { /** */ + public void removeAllCalcIdParam( + ) { + this._calcIdParamList.clear(); + } + + /** + */ public void removeAllHiddenColumns( ) { this._hiddenColumnsList.clear(); } /** + * Method removeCalcIdParam. + * + * @param vCalcIdParam + * @return true if the object was removed from the collection. + */ + public boolean removeCalcIdParam( + final jalview.schemabinding.version2.CalcIdParam vCalcIdParam) { + boolean removed = _calcIdParamList.remove(vCalcIdParam); + return removed; + } + + /** + * Method removeCalcIdParamAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.CalcIdParam removeCalcIdParamAt( + final int index) { + java.lang.Object obj = this._calcIdParamList.remove(index); + return (jalview.schemabinding.version2.CalcIdParam) obj; + } + + /** * Method removeHiddenColumns. * * @param vHiddenColumns @@ -1927,6 +2102,41 @@ public class Viewport implements java.io.Serializable { } /** + * + * + * @param index + * @param vCalcIdParam + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setCalcIdParam( + final int index, + final jalview.schemabinding.version2.CalcIdParam vCalcIdParam) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._calcIdParamList.size()) { + throw new IndexOutOfBoundsException("setCalcIdParam: Index value '" + index + "' not in range [0.." + (this._calcIdParamList.size() - 1) + "]"); + } + + this._calcIdParamList.set(index, vCalcIdParam); + } + + /** + * + * + * @param vCalcIdParamArray + */ + public void setCalcIdParam( + final jalview.schemabinding.version2.CalcIdParam[] vCalcIdParamArray) { + //-- copy array + _calcIdParamList.clear(); + + for (int i = 0; i < vCalcIdParamArray.length; i++) { + this._calcIdParamList.add(vCalcIdParamArray[i]); + } + } + + /** * Sets the value of field 'centreColumnLabels'. * * @param centreColumnLabels the value of field @@ -1939,6 +2149,20 @@ public class Viewport implements java.io.Serializable { } /** + * Sets the value of field 'complementId'. The field + * 'complementId' has the following description: The viewport + * id of this viewport's (cdna/protein) coding complement, if + * any + * + * + * @param complementId the value of field 'complementId'. + */ + public void setComplementId( + final java.lang.String complementId) { + this._complementId = complementId; + } + + /** * Sets the value of field 'consThreshold'. * * @param consThreshold the value of field 'consThreshold'. @@ -2075,7 +2299,8 @@ public class Viewport implements java.io.Serializable { /** * Sets the value of field 'id'. The field 'id' has the * following description: unique id used by jalview to - * synchronize between stored and instantiated views + * synchronize between stored and + * instantiated views * * * @param id the value of field 'id'. @@ -2098,6 +2323,18 @@ public class Viewport implements java.io.Serializable { } /** + * Sets the value of field 'normaliseSequenceLogo'. + * + * @param normaliseSequenceLogo the value of field + * 'normaliseSequenceLogo'. + */ + public void setNormaliseSequenceLogo( + final boolean normaliseSequenceLogo) { + this._normaliseSequenceLogo = normaliseSequenceLogo; + this._has_normaliseSequenceLogo = true; + } + + /** * Sets the value of field 'pidSelected'. * * @param pidSelected the value of field 'pidSelected'.