X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FSetting.java;h=59e9522efcf9e57dfdd0facc06ee2492c774c6d6;hb=aa4e99f8937ce22963cf32f1e92f174ee52ad7ee;hp=58779c509cc2c44ee1c1f59b398a6a263ada9455;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git
diff --git a/src/jalview/schemabinding/version2/Setting.java b/src/jalview/schemabinding/version2/Setting.java
index 58779c5..59e9522 100644
--- a/src/jalview/schemabinding/version2/Setting.java
+++ b/src/jalview/schemabinding/version2/Setting.java
@@ -1,22 +1,3 @@
-/*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * 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
@@ -92,6 +73,12 @@ public class Setting implements java.io.Serializable
private boolean _has_mincolour;
/**
+ * Field _noValueColour.
+ */
+ private jalview.schemabinding.version2.types.NoValueColour _noValueColour = jalview.schemabinding.version2.types.NoValueColour
+ .valueOf("Min");
+
+ /**
* threshold value for graduated feature colour
*
*/
@@ -153,6 +140,16 @@ public class Setting implements java.io.Serializable
*/
private boolean _has_autoScale;
+ /**
+ * name of feature attribute to colour by, or attribute and sub-attribute
+ */
+ private java.util.Vector _attributeNameList;
+
+ /**
+ * optional filter(s) applied to the feature type
+ */
+ private jalview.schemabinding.version2.MatcherSet _matcherSet;
+
// ----------------/
// - Constructors -/
// ----------------/
@@ -160,6 +157,9 @@ public class Setting implements java.io.Serializable
public Setting()
{
super();
+ setNoValueColour(jalview.schemabinding.version2.types.NoValueColour
+ .valueOf("Min"));
+ this._attributeNameList = new java.util.Vector();
}
// -----------/
@@ -167,76 +167,175 @@ public class Setting implements java.io.Serializable
// -----------/
/**
- */
+ *
+ *
+ * @param vAttributeName
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addAttributeName(final java.lang.String vAttributeName)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check for the maximum size
+ if (this._attributeNameList.size() >= 2)
+ {
+ throw new IndexOutOfBoundsException(
+ "addAttributeName has a maximum of 2");
+ }
+
+ this._attributeNameList.addElement(vAttributeName);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAttributeName
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addAttributeName(final int index,
+ final java.lang.String vAttributeName)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check for the maximum size
+ if (this._attributeNameList.size() >= 2)
+ {
+ throw new IndexOutOfBoundsException(
+ "addAttributeName has a maximum of 2");
+ }
+
+ this._attributeNameList.add(index, vAttributeName);
+ }
+
+ /**
+ */
public void deleteAutoScale()
{
this._has_autoScale = false;
}
/**
- */
+ */
public void deleteColour()
{
this._has_colour = false;
}
/**
- */
+ */
public void deleteColourByLabel()
{
this._has_colourByLabel = false;
}
/**
- */
+ */
public void deleteDisplay()
{
this._has_display = false;
}
/**
- */
+ */
public void deleteMax()
{
this._has_max = false;
}
/**
- */
+ */
public void deleteMin()
{
this._has_min = false;
}
/**
- */
+ */
public void deleteMincolour()
{
this._has_mincolour = false;
}
/**
- */
+ */
public void deleteOrder()
{
this._has_order = false;
}
/**
- */
+ */
public void deleteThreshold()
{
this._has_threshold = false;
}
/**
- */
+ */
public void deleteThreshstate()
{
this._has_threshstate = false;
}
/**
+ * Method enumerateAttributeName.
+ *
+ * @return an Enumeration over all java.lang.String elements
+ */
+ public java.util.Enumeration enumerateAttributeName()
+ {
+ return this._attributeNameList.elements();
+ }
+
+ /**
+ * Method getAttributeName.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the java.lang.String at the given index
+ */
+ public java.lang.String getAttributeName(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._attributeNameList.size())
+ {
+ throw new IndexOutOfBoundsException("getAttributeName: Index value '"
+ + index + "' not in range [0.."
+ + (this._attributeNameList.size() - 1) + "]");
+ }
+
+ return (java.lang.String) _attributeNameList.get(index);
+ }
+
+ /**
+ * Method getAttributeName.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 java.lang.String[] getAttributeName()
+ {
+ java.lang.String[] array = new java.lang.String[0];
+ return (java.lang.String[]) this._attributeNameList.toArray(array);
+ }
+
+ /**
+ * Method getAttributeNameCount.
+ *
+ * @return the size of this collection
+ */
+ public int getAttributeNameCount()
+ {
+ return this._attributeNameList.size();
+ }
+
+ /**
* Returns the value of field 'autoScale'.
*
* @return the value of field 'AutoScale'.
@@ -277,6 +376,17 @@ public class Setting implements java.io.Serializable
}
/**
+ * Returns the value of field 'matcherSet'. The field 'matcherSet' has the
+ * following description: optional filter(s) applied to the feature type
+ *
+ * @return the value of field 'MatcherSet'.
+ */
+ public jalview.schemabinding.version2.MatcherSet getMatcherSet()
+ {
+ return this._matcherSet;
+ }
+
+ /**
* Returns the value of field 'max'.
*
* @return the value of field 'Max'.
@@ -309,6 +419,16 @@ public class Setting implements java.io.Serializable
}
/**
+ * Returns the value of field 'noValueColour'.
+ *
+ * @return the value of field 'NoValueColour'.
+ */
+ public jalview.schemabinding.version2.types.NoValueColour getNoValueColour()
+ {
+ return this._noValueColour;
+ }
+
+ /**
* Returns the value of field 'order'.
*
* @return the value of field 'Order'.
@@ -537,6 +657,76 @@ public class Setting implements java.io.Serializable
}
/**
+ */
+ public void removeAllAttributeName()
+ {
+ this._attributeNameList.clear();
+ }
+
+ /**
+ * Method removeAttributeName.
+ *
+ * @param vAttributeName
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeAttributeName(final java.lang.String vAttributeName)
+ {
+ boolean removed = _attributeNameList.remove(vAttributeName);
+ return removed;
+ }
+
+ /**
+ * Method removeAttributeNameAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public java.lang.String removeAttributeNameAt(final int index)
+ {
+ java.lang.Object obj = this._attributeNameList.remove(index);
+ return (java.lang.String) obj;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAttributeName
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setAttributeName(final int index,
+ final java.lang.String vAttributeName)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._attributeNameList.size())
+ {
+ throw new IndexOutOfBoundsException("setAttributeName: Index value '"
+ + index + "' not in range [0.."
+ + (this._attributeNameList.size() - 1) + "]");
+ }
+
+ this._attributeNameList.set(index, vAttributeName);
+ }
+
+ /**
+ *
+ *
+ * @param vAttributeNameArray
+ */
+ public void setAttributeName(final java.lang.String[] vAttributeNameArray)
+ {
+ // -- copy array
+ _attributeNameList.clear();
+
+ for (int i = 0; i < vAttributeNameArray.length; i++)
+ {
+ this._attributeNameList.add(vAttributeNameArray[i]);
+ }
+ }
+
+ /**
* Sets the value of field 'autoScale'.
*
* @param autoScale
@@ -585,6 +775,19 @@ public class Setting implements java.io.Serializable
}
/**
+ * Sets the value of field 'matcherSet'. The field 'matcherSet' has the
+ * following description: optional filter(s) applied to the feature type
+ *
+ * @param matcherSet
+ * the value of field 'matcherSet'.
+ */
+ public void setMatcherSet(
+ final jalview.schemabinding.version2.MatcherSet matcherSet)
+ {
+ this._matcherSet = matcherSet;
+ }
+
+ /**
* Sets the value of field 'max'.
*
* @param max
@@ -623,6 +826,18 @@ public class Setting implements java.io.Serializable
}
/**
+ * Sets the value of field 'noValueColour'.
+ *
+ * @param noValueColour
+ * the value of field 'noValueColour'.
+ */
+ public void setNoValueColour(
+ final jalview.schemabinding.version2.types.NoValueColour noValueColour)
+ {
+ this._noValueColour = noValueColour;
+ }
+
+ /**
* Sets the value of field 'order'.
*
* @param order