X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FStructureState.java;h=fe7c95d99e598180f7214befd3d1bbbe1e11282e;hb=5247711ab4a6453614e2a9fb9307e6bae6a7b4a9;hp=2feb11e4c91822a396e95531b4903b33d0e0a30f;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git
diff --git a/src/jalview/schemabinding/version2/StructureState.java b/src/jalview/schemabinding/version2/StructureState.java
index 2feb11e..fe7c95d 100644
--- a/src/jalview/schemabinding/version2/StructureState.java
+++ b/src/jalview/schemabinding/version2/StructureState.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
@@ -59,21 +42,87 @@ public class StructureState implements java.io.Serializable {
private boolean _has_visible;
/**
- * additional identifier which properly disambiguates
- * the structure view from any other view with the same
- * attributes. This is not an ID,
- * because it is possible to have many references to the same
- * physical structure view
- * from different sequences in an alignment. A structureState
- * element citing the same
- * viewId will appear for each instance.
+ * additional
+ * identifier
+ * which
+ * properly
+ * disambiguates
+ * the
+ * structure
+ * view
+ * from
+ * any
+ * other
+ * view
+ * with
+ * the
+ * same
+ * attributes.
+ * This
+ * is
+ * not
+ * an
+ * ID,
+ * because
+ * it
+ * is
+ * possible
+ * to
+ * have
+ * many
+ * references
+ * to
+ * the
+ * same
+ * physical
+ * structure
+ * view
+ * from
+ * different
+ * sequences
+ * in
+ * an
+ * alignment.
+ * A
+ * structureState
+ * element
+ * citing
+ * the
+ * same
+ * viewId
+ * will
+ * appear
+ * for
+ * each
+ * instance.
+ *
*/
private java.lang.String _viewId;
/**
- * Flag set if the alignment panel containing this JSeq should
- * be included in those used to perform a structure
- * superposition (since Jalview 2.7).
+ * Flag
+ * set
+ * if
+ * the
+ * alignment
+ * panel
+ * containing
+ * this
+ * JSeq
+ * should
+ * be
+ * included
+ * in
+ * those
+ * used
+ * to
+ * perform
+ * a
+ * structure
+ * superposition
+ * (since
+ * Jalview
+ * 2.7).
*
*/
private boolean _alignwithAlignPanel = true;
@@ -84,9 +133,31 @@ public class StructureState implements java.io.Serializable {
private boolean _has_alignwithAlignPanel;
/**
- * Flag set if the alignment panel containing this JSeq should
- * be included in those used to colour its associated sequences
- * in this structureState(since Jalview 2.7).
+ * Flag
+ * set
+ * if
+ * the
+ * alignment
+ * panel
+ * containing
+ * this
+ * JSeq
+ * should
+ * be
+ * included
+ * in
+ * those
+ * used
+ * to
+ * colour
+ * its
+ * associated
+ * sequences
+ * in
+ * this
+ * structureState(since
+ * Jalview
+ * 2.7).
*
*/
private boolean _colourwithAlignPanel = false;
@@ -97,8 +168,27 @@ public class StructureState implements java.io.Serializable {
private boolean _has_colourwithAlignPanel;
/**
- * Flag set if the structure display is coloured by the Jmol
- * state, rather than by one or more linked alignment views.
+ * Flag
+ * set
+ * if
+ * the
+ * structure
+ * display
+ * is
+ * coloured
+ * by
+ * the
+ * Jmol
+ * state,
+ * rather
+ * than
+ * by
+ * one
+ * or
+ * more
+ * linked
+ * alignment
+ * views.
*
*/
private boolean _colourByJmol = true;
@@ -109,6 +199,22 @@ public class StructureState implements java.io.Serializable {
private boolean _has_colourByJmol;
/**
+ * An
+ * identifier
+ * for
+ * the
+ * viewer
+ * type,
+ * currently
+ * either
+ * JMOL
+ * or
+ * CHIMERA
+ *
+ */
+ private java.lang.String _type;
+
+ /**
* Field _width.
*/
private int _width;
@@ -222,9 +328,28 @@ public class StructureState implements java.io.Serializable {
/**
* Returns the value of field 'alignwithAlignPanel'. The field
* 'alignwithAlignPanel' has the following description: Flag
- * set if the alignment panel containing this JSeq should be
- * included in those used to perform a structure superposition
- * (since Jalview 2.7).
+ * set
+ * if
+ * the
+ * alignment
+ * panel
+ * containing
+ * this
+ * JSeq
+ * should
+ * be
+ * included
+ * in
+ * those
+ * used
+ * to
+ * perform
+ * a
+ * structure
+ * superposition
+ * (since
+ * Jalview
+ * 2.7).
*
*
* @return the value of field 'AlignwithAlignPanel'.
@@ -236,9 +361,27 @@ public class StructureState implements java.io.Serializable {
/**
* Returns the value of field 'colourByJmol'. The field
- * 'colourByJmol' has the following description: Flag set if
- * the structure display is coloured by the Jmol state, rather
- * than by one or more linked alignment views.
+ * 'colourByJmol' has the following description: Flag
+ * set
+ * if
+ * the
+ * structure
+ * display
+ * is
+ * coloured
+ * by
+ * the
+ * Jmol
+ * state,
+ * rather
+ * than
+ * by
+ * one
+ * or
+ * more
+ * linked
+ * alignment
+ * views.
*
*
* @return the value of field 'ColourByJmol'.
@@ -251,9 +394,30 @@ public class StructureState implements java.io.Serializable {
/**
* Returns the value of field 'colourwithAlignPanel'. The field
* 'colourwithAlignPanel' has the following description: Flag
- * set if the alignment panel containing this JSeq should be
- * included in those used to colour its associated sequences in
- * this structureState(since Jalview 2.7).
+ * set
+ * if
+ * the
+ * alignment
+ * panel
+ * containing
+ * this
+ * JSeq
+ * should
+ * be
+ * included
+ * in
+ * those
+ * used
+ * to
+ * colour
+ * its
+ * associated
+ * sequences
+ * in
+ * this
+ * structureState(since
+ * Jalview
+ * 2.7).
*
*
* @return the value of field 'ColourwithAlignPanel'.
@@ -285,16 +449,83 @@ public class StructureState implements java.io.Serializable {
}
/**
+ * Returns the value of field 'type'. The field 'type' has the
+ * following description: An
+ * identifier
+ * for
+ * the
+ * viewer
+ * type,
+ * currently
+ * either
+ * JMOL
+ * or
+ * CHIMERA
+ *
+ *
+ * @return the value of field 'Type'.
+ */
+ public java.lang.String getType(
+ ) {
+ return this._type;
+ }
+
+ /**
* Returns the value of field 'viewId'. The field 'viewId' has
- * the following description: additional identifier which
- * properly disambiguates
- * the structure view from any other view with the same
- * attributes. This is not an ID,
- * because it is possible to have many references to the same
- * physical structure view
- * from different sequences in an alignment. A structureState
- * element citing the same
- * viewId will appear for each instance.
+ * the following description: additional
+ * identifier
+ * which
+ * properly
+ * disambiguates
+ * the
+ * structure
+ * view
+ * from
+ * any
+ * other
+ * view
+ * with
+ * the
+ * same
+ * attributes.
+ * This
+ * is
+ * not
+ * an
+ * ID,
+ * because
+ * it
+ * is
+ * possible
+ * to
+ * have
+ * many
+ * references
+ * to
+ * the
+ * same
+ * physical
+ * structure
+ * view
+ * from
+ * different
+ * sequences
+ * in
+ * an
+ * alignment.
+ * A
+ * structureState
+ * element
+ * citing
+ * the
+ * same
+ * viewId
+ * will
+ * appear
+ * for
+ * each
+ * instance.
+ *
*
* @return the value of field 'ViewId'.
*/
@@ -428,9 +659,28 @@ public class StructureState implements java.io.Serializable {
/**
* Returns the value of field 'alignwithAlignPanel'. The field
* 'alignwithAlignPanel' has the following description: Flag
- * set if the alignment panel containing this JSeq should be
- * included in those used to perform a structure superposition
- * (since Jalview 2.7).
+ * set
+ * if
+ * the
+ * alignment
+ * panel
+ * containing
+ * this
+ * JSeq
+ * should
+ * be
+ * included
+ * in
+ * those
+ * used
+ * to
+ * perform
+ * a
+ * structure
+ * superposition
+ * (since
+ * Jalview
+ * 2.7).
*
*
* @return the value of field 'AlignwithAlignPanel'.
@@ -442,9 +692,27 @@ public class StructureState implements java.io.Serializable {
/**
* Returns the value of field 'colourByJmol'. The field
- * 'colourByJmol' has the following description: Flag set if
- * the structure display is coloured by the Jmol state, rather
- * than by one or more linked alignment views.
+ * 'colourByJmol' has the following description: Flag
+ * set
+ * if
+ * the
+ * structure
+ * display
+ * is
+ * coloured
+ * by
+ * the
+ * Jmol
+ * state,
+ * rather
+ * than
+ * by
+ * one
+ * or
+ * more
+ * linked
+ * alignment
+ * views.
*
*
* @return the value of field 'ColourByJmol'.
@@ -457,9 +725,30 @@ public class StructureState implements java.io.Serializable {
/**
* Returns the value of field 'colourwithAlignPanel'. The field
* 'colourwithAlignPanel' has the following description: Flag
- * set if the alignment panel containing this JSeq should be
- * included in those used to colour its associated sequences in
- * this structureState(since Jalview 2.7).
+ * set
+ * if
+ * the
+ * alignment
+ * panel
+ * containing
+ * this
+ * JSeq
+ * should
+ * be
+ * included
+ * in
+ * those
+ * used
+ * to
+ * colour
+ * its
+ * associated
+ * sequences
+ * in
+ * this
+ * structureState(since
+ * Jalview
+ * 2.7).
*
*
* @return the value of field 'ColourwithAlignPanel'.
@@ -529,9 +818,28 @@ public class StructureState implements java.io.Serializable {
/**
* Sets the value of field 'alignwithAlignPanel'. The field
* 'alignwithAlignPanel' has the following description: Flag
- * set if the alignment panel containing this JSeq should be
- * included in those used to perform a structure superposition
- * (since Jalview 2.7).
+ * set
+ * if
+ * the
+ * alignment
+ * panel
+ * containing
+ * this
+ * JSeq
+ * should
+ * be
+ * included
+ * in
+ * those
+ * used
+ * to
+ * perform
+ * a
+ * structure
+ * superposition
+ * (since
+ * Jalview
+ * 2.7).
*
*
* @param alignwithAlignPanel the value of field
@@ -545,9 +853,27 @@ public class StructureState implements java.io.Serializable {
/**
* Sets the value of field 'colourByJmol'. The field
- * 'colourByJmol' has the following description: Flag set if
- * the structure display is coloured by the Jmol state, rather
- * than by one or more linked alignment views.
+ * 'colourByJmol' has the following description: Flag
+ * set
+ * if
+ * the
+ * structure
+ * display
+ * is
+ * coloured
+ * by
+ * the
+ * Jmol
+ * state,
+ * rather
+ * than
+ * by
+ * one
+ * or
+ * more
+ * linked
+ * alignment
+ * views.
*
*
* @param colourByJmol the value of field 'colourByJmol'.
@@ -561,9 +887,30 @@ public class StructureState implements java.io.Serializable {
/**
* Sets the value of field 'colourwithAlignPanel'. The field
* 'colourwithAlignPanel' has the following description: Flag
- * set if the alignment panel containing this JSeq should be
- * included in those used to colour its associated sequences in
- * this structureState(since Jalview 2.7).
+ * set
+ * if
+ * the
+ * alignment
+ * panel
+ * containing
+ * this
+ * JSeq
+ * should
+ * be
+ * included
+ * in
+ * those
+ * used
+ * to
+ * colour
+ * its
+ * associated
+ * sequences
+ * in
+ * this
+ * structureState(since
+ * Jalview
+ * 2.7).
*
*
* @param colourwithAlignPanel the value of field
@@ -598,16 +945,83 @@ public class StructureState implements java.io.Serializable {
}
/**
+ * Sets the value of field 'type'. The field 'type' has the
+ * following description: An
+ * identifier
+ * for
+ * the
+ * viewer
+ * type,
+ * currently
+ * either
+ * JMOL
+ * or
+ * CHIMERA
+ *
+ *
+ * @param type the value of field 'type'.
+ */
+ public void setType(
+ final java.lang.String type) {
+ this._type = type;
+ }
+
+ /**
* Sets the value of field 'viewId'. The field 'viewId' has the
- * following description: additional identifier which properly
- * disambiguates
- * the structure view from any other view with the same
- * attributes. This is not an ID,
- * because it is possible to have many references to the same
- * physical structure view
- * from different sequences in an alignment. A structureState
- * element citing the same
- * viewId will appear for each instance.
+ * following description: additional
+ * identifier
+ * which
+ * properly
+ * disambiguates
+ * the
+ * structure
+ * view
+ * from
+ * any
+ * other
+ * view
+ * with
+ * the
+ * same
+ * attributes.
+ * This
+ * is
+ * not
+ * an
+ * ID,
+ * because
+ * it
+ * is
+ * possible
+ * to
+ * have
+ * many
+ * references
+ * to
+ * the
+ * same
+ * physical
+ * structure
+ * view
+ * from
+ * different
+ * sequences
+ * in
+ * an
+ * alignment.
+ * A
+ * structureState
+ * element
+ * citing
+ * the
+ * same
+ * viewId
+ * will
+ * appear
+ * for
+ * each
+ * instance.
+ *
*
* @param viewId the value of field 'viewId'.
*/