X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FViewport.java;h=159f7ae9ccb074ad5d38a3a72d57dc908a9d7560;hb=8adf4aca94b4eddf964960b3706368245a8ad485;hp=1faf480a3150a05f0ba15c141f11300b15aee16a;hpb=aced09c4feeaf3406269442c14e54abeeb4cad81;p=jalview.git
diff --git a/src/jalview/schemabinding/version2/Viewport.java b/src/jalview/schemabinding/version2/Viewport.java
index 1faf480..159f7ae 100644
--- a/src/jalview/schemabinding/version2/Viewport.java
+++ b/src/jalview/schemabinding/version2/Viewport.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;
@@ -347,6 +332,16 @@ public class Viewport implements java.io.Serializable
private boolean _has_fontStyle;
/**
+ * Field _scaleProteinAsCdna.
+ */
+ private boolean _scaleProteinAsCdna = true;
+
+ /**
+ * keeps track of state for field: _scaleProteinAsCdna
+ */
+ private boolean _has_scaleProteinAsCdna;
+
+ /**
* Field _viewName.
*/
private java.lang.String _viewName;
@@ -404,6 +399,12 @@ public class Viewport implements java.io.Serializable
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;
@@ -638,6 +639,13 @@ public class Viewport implements java.io.Serializable
/**
*/
+ public void deleteScaleProteinAsCdna()
+ {
+ this._has_scaleProteinAsCdna = false;
+ }
+
+ /**
+ */
public void deleteShowAnnotation()
{
this._has_showAnnotation = false;
@@ -847,11 +855,9 @@ public class Viewport implements java.io.Serializable
// check bounds for index
if (index < 0 || index >= this._calcIdParamList.size())
{
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "getCalcIdParam",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._calcIdParamList.size() - 1)).toString()
- }));
+ throw new IndexOutOfBoundsException("getCalcIdParam: Index value '"
+ + index + "' not in range [0.."
+ + (this._calcIdParamList.size() - 1) + "]");
}
return (jalview.schemabinding.version2.CalcIdParam) _calcIdParamList
@@ -895,6 +901,19 @@ 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'.
@@ -999,11 +1018,9 @@ public class Viewport implements java.io.Serializable
// check bounds for index
if (index < 0 || index >= this._hiddenColumnsList.size())
{
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "getHiddenColumns",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._hiddenColumnsList.size() - 1)).toString()
- }));
+ throw new IndexOutOfBoundsException("getHiddenColumns: Index value '"
+ + index + "' not in range [0.."
+ + (this._hiddenColumnsList.size() - 1) + "]");
}
return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList
@@ -1110,6 +1127,16 @@ public class Viewport implements java.io.Serializable
}
/**
+ * Returns the value of field 'scaleProteinAsCdna'.
+ *
+ * @return the value of field 'ScaleProteinAsCdna'.
+ */
+ public boolean getScaleProteinAsCdna()
+ {
+ return this._scaleProteinAsCdna;
+ }
+
+ /**
* Returns the value of field 'sequenceSetId'.
*
* @return the value of field 'SequenceSetId'.
@@ -1510,6 +1537,16 @@ public class Viewport implements java.io.Serializable
}
/**
+ * Method hasScaleProteinAsCdna.
+ *
+ * @return true if at least one ScaleProteinAsCdna has been adde
+ */
+ public boolean hasScaleProteinAsCdna()
+ {
+ return this._has_scaleProteinAsCdna;
+ }
+
+ /**
* Method hasShowAnnotation.
*
* @return true if at least one ShowAnnotation has been added
@@ -1830,6 +1867,16 @@ public class Viewport implements java.io.Serializable
}
/**
+ * Returns the value of field 'scaleProteinAsCdna'.
+ *
+ * @return the value of field 'ScaleProteinAsCdna'.
+ */
+ public boolean isScaleProteinAsCdna()
+ {
+ return this._scaleProteinAsCdna;
+ }
+
+ /**
* Returns the value of field 'showAnnotation'.
*
* @return the value of field 'ShowAnnotation'.
@@ -2127,11 +2174,9 @@ public class Viewport implements java.io.Serializable
// check bounds for index
if (index < 0 || index >= this._calcIdParamList.size())
{
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "setCalcIdParam",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._calcIdParamList.size() - 1)).toString()
- }));
+ throw new IndexOutOfBoundsException("setCalcIdParam: Index value '"
+ + index + "' not in range [0.."
+ + (this._calcIdParamList.size() - 1) + "]");
}
this._calcIdParamList.set(index, vCalcIdParam);
@@ -2167,6 +2212,20 @@ 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
@@ -2288,11 +2347,9 @@ public class Viewport implements java.io.Serializable
// check bounds for index
if (index < 0 || index >= this._hiddenColumnsList.size())
{
- throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
- "setHiddenColumns",
- Integer.valueOf(index).toString(),
- Integer.valueOf((this._hiddenColumnsList.size() - 1)).toString()
- }));
+ throw new IndexOutOfBoundsException("setHiddenColumns: Index value '"
+ + index + "' not in range [0.."
+ + (this._hiddenColumnsList.size() - 1) + "]");
}
this._hiddenColumnsList.set(index, vHiddenColumns);
@@ -2402,6 +2459,18 @@ public class Viewport implements java.io.Serializable
}
/**
+ * Sets the value of field 'scaleProteinAsCdna'.
+ *
+ * @param scaleProteinAsCdna
+ * the value of field 'scaleProteinAsCdna'.
+ */
+ public void setScaleProteinAsCdna(final boolean scaleProteinAsCdna)
+ {
+ this._scaleProteinAsCdna = scaleProteinAsCdna;
+ this._has_scaleProteinAsCdna = true;
+ }
+
+ /**
* Sets the value of field 'sequenceSetId'.
*
* @param sequenceSetId