X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FStructureState.java;h=2feb11e4c91822a396e95531b4903b33d0e0a30f;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=6f4310838f101855145cd5b04ad413d2354fa218;hpb=cd07a161a10680208029f76aa46710c1032aae46;p=jalview.git
diff --git a/src/jalview/schemabinding/version2/StructureState.java b/src/jalview/schemabinding/version2/StructureState.java
index 6f43108..2feb11e 100644
--- a/src/jalview/schemabinding/version2/StructureState.java
+++ b/src/jalview/schemabinding/version2/StructureState.java
@@ -1,3 +1,20 @@
+/*******************************************************************************
+ * 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
@@ -42,24 +59,54 @@ public class StructureState implements java.io.Serializable {
private boolean _has_visible;
/**
- * Field _xpos.
+ * 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 int _xpos;
+ private java.lang.String _viewId;
/**
- * keeps track of state for field: _xpos
+ * 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 _has_xpos;
+ private boolean _alignwithAlignPanel = true;
/**
- * Field _ypos.
+ * keeps track of state for field: _alignwithAlignPanel
*/
- private int _ypos;
+ private boolean _has_alignwithAlignPanel;
/**
- * keeps track of state for field: _ypos
+ * 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 _has_ypos;
+ private boolean _colourwithAlignPanel = false;
+
+ /**
+ * keeps track of state for field: _colourwithAlignPanel
+ */
+ 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.
+ *
+ */
+ private boolean _colourByJmol = true;
+
+ /**
+ * keeps track of state for field: _colourByJmol
+ */
+ private boolean _has_colourByJmol;
/**
* Field _width.
@@ -82,9 +129,24 @@ public class StructureState implements java.io.Serializable {
private boolean _has_height;
/**
- * Field _viewId.
+ * Field _xpos.
*/
- private java.lang.String _viewId;
+ private int _xpos;
+
+ /**
+ * keeps track of state for field: _xpos
+ */
+ private boolean _has_xpos;
+
+ /**
+ * Field _ypos.
+ */
+ private int _ypos;
+
+ /**
+ * keeps track of state for field: _ypos
+ */
+ private boolean _has_ypos;
//----------------/
@@ -103,6 +165,27 @@ public class StructureState implements java.io.Serializable {
/**
*/
+ public void deleteAlignwithAlignPanel(
+ ) {
+ this._has_alignwithAlignPanel= false;
+ }
+
+ /**
+ */
+ public void deleteColourByJmol(
+ ) {
+ this._has_colourByJmol= false;
+ }
+
+ /**
+ */
+ public void deleteColourwithAlignPanel(
+ ) {
+ this._has_colourwithAlignPanel= false;
+ }
+
+ /**
+ */
public void deleteHeight(
) {
this._has_height= false;
@@ -137,6 +220,50 @@ 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).
+ *
+ *
+ * @return the value of field 'AlignwithAlignPanel'.
+ */
+ public boolean getAlignwithAlignPanel(
+ ) {
+ return this._alignwithAlignPanel;
+ }
+
+ /**
+ * 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.
+ *
+ *
+ * @return the value of field 'ColourByJmol'.
+ */
+ public boolean getColourByJmol(
+ ) {
+ return this._colourByJmol;
+ }
+
+ /**
+ * 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).
+ *
+ *
+ * @return the value of field 'ColourwithAlignPanel'.
+ */
+ public boolean getColourwithAlignPanel(
+ ) {
+ return this._colourwithAlignPanel;
+ }
+
+ /**
* Returns the value of field 'content'. The field 'content'
* has the following description: internal content storage
*
@@ -158,7 +285,16 @@ public class StructureState implements java.io.Serializable {
}
/**
- * Returns the value of field 'viewId'.
+ * 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.
*
* @return the value of field 'ViewId'.
*/
@@ -208,6 +344,38 @@ public class StructureState implements java.io.Serializable {
}
/**
+ * Method hasAlignwithAlignPanel.
+ *
+ * @return true if at least one AlignwithAlignPanel has been
+ * added
+ */
+ public boolean hasAlignwithAlignPanel(
+ ) {
+ return this._has_alignwithAlignPanel;
+ }
+
+ /**
+ * Method hasColourByJmol.
+ *
+ * @return true if at least one ColourByJmol has been added
+ */
+ public boolean hasColourByJmol(
+ ) {
+ return this._has_colourByJmol;
+ }
+
+ /**
+ * Method hasColourwithAlignPanel.
+ *
+ * @return true if at least one ColourwithAlignPanel has been
+ * added
+ */
+ public boolean hasColourwithAlignPanel(
+ ) {
+ return this._has_colourwithAlignPanel;
+ }
+
+ /**
* Method hasHeight.
*
* @return true if at least one Height has been added
@@ -258,6 +426,50 @@ 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).
+ *
+ *
+ * @return the value of field 'AlignwithAlignPanel'.
+ */
+ public boolean isAlignwithAlignPanel(
+ ) {
+ return this._alignwithAlignPanel;
+ }
+
+ /**
+ * 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.
+ *
+ *
+ * @return the value of field 'ColourByJmol'.
+ */
+ public boolean isColourByJmol(
+ ) {
+ return this._colourByJmol;
+ }
+
+ /**
+ * 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).
+ *
+ *
+ * @return the value of field 'ColourwithAlignPanel'.
+ */
+ public boolean isColourwithAlignPanel(
+ ) {
+ return this._colourwithAlignPanel;
+ }
+
+ /**
* Method isValid.
*
* @return true if this object is valid according to the schema
@@ -315,6 +527,55 @@ 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).
+ *
+ *
+ * @param alignwithAlignPanel the value of field
+ * 'alignwithAlignPanel'.
+ */
+ public void setAlignwithAlignPanel(
+ final boolean alignwithAlignPanel) {
+ this._alignwithAlignPanel = alignwithAlignPanel;
+ this._has_alignwithAlignPanel = true;
+ }
+
+ /**
+ * 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.
+ *
+ *
+ * @param colourByJmol the value of field 'colourByJmol'.
+ */
+ public void setColourByJmol(
+ final boolean colourByJmol) {
+ this._colourByJmol = colourByJmol;
+ this._has_colourByJmol = true;
+ }
+
+ /**
+ * 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).
+ *
+ *
+ * @param colourwithAlignPanel the value of field
+ * 'colourwithAlignPanel'.
+ */
+ public void setColourwithAlignPanel(
+ final boolean colourwithAlignPanel) {
+ this._colourwithAlignPanel = colourwithAlignPanel;
+ this._has_colourwithAlignPanel = true;
+ }
+
+ /**
* Sets the value of field 'content'. The field 'content' has
* the following description: internal content storage
*
@@ -337,7 +598,16 @@ public class StructureState implements java.io.Serializable {
}
/**
- * Sets the value of field 'viewId'.
+ * 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.
*
* @param viewId the value of field 'viewId'.
*/