X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FJalviewModelSequence.java;h=932ba14a32f8ed8cfac36208f4fa0038c8b9b3a2;hb=06827cdbf16226b2a625f6a94bde942b0e74b770;hp=790a1cabc37096c7fa616b39a257454ec626eb71;hpb=aced09c4feeaf3406269442c14e54abeeb4cad81;p=jalview.git diff --git a/src/jalview/schemabinding/version2/JalviewModelSequence.java b/src/jalview/schemabinding/version2/JalviewModelSequence.java index 790a1ca..932ba14 100644 --- a/src/jalview/schemabinding/version2/JalviewModelSequence.java +++ b/src/jalview/schemabinding/version2/JalviewModelSequence.java @@ -1,31 +1,16 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors - * - * 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 . - * The Jalview Authors are detailed in the 'AUTHORS' file. + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2; //---------------------------------/ //- Imported classes and packages -/ //---------------------------------/ -import jalview.util.MessageManager; - import org.exolab.castor.xml.Marshaller; import org.exolab.castor.xml.Unmarshaller; @@ -67,6 +52,11 @@ public class JalviewModelSequence implements java.io.Serializable private java.util.Vector _treeList; /** + * Field _pcaViewerList. + */ + private java.util.Vector _pcaViewerList; + + /** * Field _featureSettings. */ private jalview.schemabinding.version2.FeatureSettings _featureSettings; @@ -83,6 +73,7 @@ public class JalviewModelSequence implements java.io.Serializable this._viewportList = new java.util.Vector(); this._userColoursList = new java.util.Vector(); this._treeList = new java.util.Vector(); + this._pcaViewerList = new java.util.Vector(); } // -----------/ @@ -148,6 +139,35 @@ public class JalviewModelSequence implements java.io.Serializable /** * * + * @param vPcaViewer + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addPcaViewer( + final jalview.schemabinding.version2.PcaViewer vPcaViewer) + throws java.lang.IndexOutOfBoundsException + { + this._pcaViewerList.addElement(vPcaViewer); + } + + /** + * + * + * @param index + * @param vPcaViewer + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addPcaViewer(final int index, + final jalview.schemabinding.version2.PcaViewer vPcaViewer) + throws java.lang.IndexOutOfBoundsException + { + this._pcaViewerList.add(index, vPcaViewer); + } + + /** + * + * * @param vTree * @throws java.lang.IndexOutOfBoundsException * if the index given is outside the bounds of the collection @@ -254,6 +274,17 @@ public class JalviewModelSequence implements java.io.Serializable } /** + * Method enumeratePcaViewer. + * + * @return an Enumeration over all jalview.schemabinding.version2.PcaViewer + * elements + */ + public java.util.Enumeration enumeratePcaViewer() + { + return this._pcaViewerList.elements(); + } + + /** * Method enumerateTree. * * @return an Enumeration over all jalview.schemabinding.version2.Tree @@ -311,11 +342,9 @@ public class JalviewModelSequence implements java.io.Serializable // check bounds for index if (index < 0 || index >= this._JGroupList.size()) { - throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{ - "getJGroup", - Integer.valueOf(index).toString(), - Integer.valueOf((this._JGroupList.size() - 1)).toString() - })); + throw new IndexOutOfBoundsException( + "getJGroup: Index value '" + index + "' not in range [0.." + + (this._JGroupList.size() - 1) + "]"); } return (jalview.schemabinding.version2.JGroup) _JGroupList.get(index); @@ -362,11 +391,8 @@ public class JalviewModelSequence implements java.io.Serializable // check bounds for index if (index < 0 || index >= this._JSeqList.size()) { - throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{ - "getJSeq", - Integer.valueOf(index).toString(), - Integer.valueOf((this._JSeqList.size() - 1)).toString() - })); + throw new IndexOutOfBoundsException("getJSeq: Index value '" + index + + "' not in range [0.." + (this._JSeqList.size() - 1) + "]"); } return (jalview.schemabinding.version2.JSeq) _JSeqList.get(index); @@ -399,6 +425,56 @@ public class JalviewModelSequence implements java.io.Serializable } /** + * Method getPcaViewer. + * + * @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.PcaViewer at the + * given index + */ + public jalview.schemabinding.version2.PcaViewer getPcaViewer( + final int index) throws java.lang.IndexOutOfBoundsException + { + // check bounds for index + if (index < 0 || index >= this._pcaViewerList.size()) + { + throw new IndexOutOfBoundsException( + "getPcaViewer: Index value '" + index + "' not in range [0.." + + (this._pcaViewerList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.PcaViewer) _pcaViewerList + .get(index); + } + + /** + * Method getPcaViewer.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.PcaViewer[] getPcaViewer() + { + jalview.schemabinding.version2.PcaViewer[] array = new jalview.schemabinding.version2.PcaViewer[0]; + return (jalview.schemabinding.version2.PcaViewer[]) this._pcaViewerList + .toArray(array); + } + + /** + * Method getPcaViewerCount. + * + * @return the size of this collection + */ + public int getPcaViewerCount() + { + return this._pcaViewerList.size(); + } + + /** * Method getTree. * * @param index @@ -413,11 +489,8 @@ public class JalviewModelSequence implements java.io.Serializable // check bounds for index if (index < 0 || index >= this._treeList.size()) { - throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{ - "getJgetTreeSeq", - Integer.valueOf(index).toString(), - Integer.valueOf((this._treeList.size() - 1)).toString() - })); + throw new IndexOutOfBoundsException("getTree: Index value '" + index + + "' not in range [0.." + (this._treeList.size() - 1) + "]"); } return (jalview.schemabinding.version2.Tree) _treeList.get(index); @@ -464,11 +537,9 @@ public class JalviewModelSequence implements java.io.Serializable // check bounds for index if (index < 0 || index >= this._userColoursList.size()) { - throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{ - "getUserColours", - Integer.valueOf(index).toString(), - Integer.valueOf((this._userColoursList.size() - 1)).toString() - })); + throw new IndexOutOfBoundsException("getUserColours: Index value '" + + index + "' not in range [0.." + + (this._userColoursList.size() - 1) + "]"); } return (jalview.schemabinding.version2.UserColours) _userColoursList @@ -510,17 +581,15 @@ public class JalviewModelSequence implements java.io.Serializable * @return the value of the jalview.schemabinding.version2.Viewport at the * given index */ - public jalview.schemabinding.version2.Viewport getViewport(final int index) - throws java.lang.IndexOutOfBoundsException + public jalview.schemabinding.version2.Viewport getViewport( + final int index) throws java.lang.IndexOutOfBoundsException { // check bounds for index if (index < 0 || index >= this._viewportList.size()) { - throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{ - "getViewport", - Integer.valueOf(index).toString(), - Integer.valueOf((this._viewportList.size() - 1)).toString() - })); + throw new IndexOutOfBoundsException( + "getViewport: Index value '" + index + "' not in range [0.." + + (this._viewportList.size() - 1) + "]"); } return (jalview.schemabinding.version2.Viewport) _viewportList @@ -608,35 +677,42 @@ public class JalviewModelSequence implements java.io.Serializable } /** - */ + */ public void removeAllJGroup() { this._JGroupList.clear(); } /** - */ + */ public void removeAllJSeq() { this._JSeqList.clear(); } /** - */ + */ + public void removeAllPcaViewer() + { + this._pcaViewerList.clear(); + } + + /** + */ public void removeAllTree() { this._treeList.clear(); } /** - */ + */ public void removeAllUserColours() { this._userColoursList.clear(); } /** - */ + */ public void removeAllViewport() { this._viewportList.clear(); @@ -693,6 +769,32 @@ public class JalviewModelSequence implements java.io.Serializable } /** + * Method removePcaViewer. + * + * @param vPcaViewer + * @return true if the object was removed from the collection. + */ + public boolean removePcaViewer( + final jalview.schemabinding.version2.PcaViewer vPcaViewer) + { + boolean removed = _pcaViewerList.remove(vPcaViewer); + return removed; + } + + /** + * Method removePcaViewerAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.PcaViewer removePcaViewerAt( + final int index) + { + java.lang.Object obj = this._pcaViewerList.remove(index); + return (jalview.schemabinding.version2.PcaViewer) obj; + } + + /** * Method removeTree. * * @param vTree @@ -795,11 +897,9 @@ public class JalviewModelSequence implements java.io.Serializable // check bounds for index if (index < 0 || index >= this._JGroupList.size()) { - throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{ - "setJGroup", - Integer.valueOf(index).toString(), - Integer.valueOf((this._JGroupList.size() - 1)).toString() - })); + throw new IndexOutOfBoundsException( + "setJGroup: Index value '" + index + "' not in range [0.." + + (this._JGroupList.size() - 1) + "]"); } this._JGroupList.set(index, vJGroup); @@ -837,11 +937,8 @@ public class JalviewModelSequence implements java.io.Serializable // check bounds for index if (index < 0 || index >= this._JSeqList.size()) { - throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{ - "setJSeq", - Integer.valueOf(index).toString(), - Integer.valueOf((this._JSeqList.size() - 1)).toString() - })); + throw new IndexOutOfBoundsException("setJSeq: Index value '" + index + + "' not in range [0.." + (this._JSeqList.size() - 1) + "]"); } this._JSeqList.set(index, vJSeq); @@ -852,7 +949,8 @@ public class JalviewModelSequence implements java.io.Serializable * * @param vJSeqArray */ - public void setJSeq(final jalview.schemabinding.version2.JSeq[] vJSeqArray) + public void setJSeq( + final jalview.schemabinding.version2.JSeq[] vJSeqArray) { // -- copy array _JSeqList.clear(); @@ -867,6 +965,46 @@ public class JalviewModelSequence implements java.io.Serializable * * * @param index + * @param vPcaViewer + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void setPcaViewer(final int index, + final jalview.schemabinding.version2.PcaViewer vPcaViewer) + throws java.lang.IndexOutOfBoundsException + { + // check bounds for index + if (index < 0 || index >= this._pcaViewerList.size()) + { + throw new IndexOutOfBoundsException( + "setPcaViewer: Index value '" + index + "' not in range [0.." + + (this._pcaViewerList.size() - 1) + "]"); + } + + this._pcaViewerList.set(index, vPcaViewer); + } + + /** + * + * + * @param vPcaViewerArray + */ + public void setPcaViewer( + final jalview.schemabinding.version2.PcaViewer[] vPcaViewerArray) + { + // -- copy array + _pcaViewerList.clear(); + + for (int i = 0; i < vPcaViewerArray.length; i++) + { + this._pcaViewerList.add(vPcaViewerArray[i]); + } + } + + /** + * + * + * @param index * @param vTree * @throws java.lang.IndexOutOfBoundsException * if the index given is outside the bounds of the collection @@ -878,11 +1016,8 @@ public class JalviewModelSequence implements java.io.Serializable // check bounds for index if (index < 0 || index >= this._treeList.size()) { - throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{ - "setTree", - Integer.valueOf(index).toString(), - Integer.valueOf((this._treeList.size() - 1)).toString() - })); + throw new IndexOutOfBoundsException("setTree: Index value '" + index + + "' not in range [0.." + (this._treeList.size() - 1) + "]"); } this._treeList.set(index, vTree); @@ -893,7 +1028,8 @@ public class JalviewModelSequence implements java.io.Serializable * * @param vTreeArray */ - public void setTree(final jalview.schemabinding.version2.Tree[] vTreeArray) + public void setTree( + final jalview.schemabinding.version2.Tree[] vTreeArray) { // -- copy array _treeList.clear(); @@ -919,11 +1055,9 @@ public class JalviewModelSequence implements java.io.Serializable // check bounds for index if (index < 0 || index >= this._userColoursList.size()) { - throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{ - "setUserColours", - Integer.valueOf(index).toString(), - Integer.valueOf((this._userColoursList.size() - 1)).toString() - })); + throw new IndexOutOfBoundsException("setUserColours: Index value '" + + index + "' not in range [0.." + + (this._userColoursList.size() - 1) + "]"); } this._userColoursList.set(index, vUserColours); @@ -961,11 +1095,9 @@ public class JalviewModelSequence implements java.io.Serializable // check bounds for index if (index < 0 || index >= this._viewportList.size()) { - throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{ - "setViewport", - Integer.valueOf(index).toString(), - Integer.valueOf((this._viewportList.size() - 1)).toString() - })); + throw new IndexOutOfBoundsException( + "setViewport: Index value '" + index + "' not in range [0.." + + (this._viewportList.size() - 1) + "]"); } this._viewportList.set(index, vViewport);