X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FViewport.java;h=7dcb3eeac28b447d9e982056abddce8fe45e3f33;hb=a23cc416cd520ac6dec6052591575b264f5d25bc;hp=0db130f18cdc9f1255003cd73783d4c8d2d08205;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git
diff --git a/src/jalview/schemabinding/version2/Viewport.java b/src/jalview/schemabinding/version2/Viewport.java
index 0db130f..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, 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
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'.