X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fbinding%2FColour.java;h=f51e9aff95ddcfe3783a5d325e5f65a626fb3f56;hb=9ee61e0b05f215f6ffa0eb33d65d7b2023ff9bad;hp=d29c1ede943ee50164c0b2c8d1df054e3f23ad07;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git
diff --git a/src/jalview/binding/Colour.java b/src/jalview/binding/Colour.java
index d29c1ed..f51e9af 100644
--- a/src/jalview/binding/Colour.java
+++ b/src/jalview/binding/Colour.java
@@ -1,20 +1,10 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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
+ * 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'. @@ -205,7 +308,9 @@ public class Colour implements java.io.Serializable } /** - * Returns the value of field 'name'. + * Returns the value of field 'name'. The field 'name' has the following + * description: Single letter residue code for an alignment colour scheme, or + * feature type for a feature colour scheme * * @return the value of field 'Name'. */ @@ -215,6 +320,16 @@ public class Colour implements java.io.Serializable } /** + * Returns the value of field 'noValueColour'. + * + * @return the value of field 'NoValueColour'. + */ + public jalview.binding.types.NoValueColour getNoValueColour() + { + return this._noValueColour; + } + + /** * Returns the value of field 'RGB'. * * @return the value of field 'RGB'. @@ -225,12 +340,11 @@ public class Colour implements java.io.Serializable } /** - * Returns the value of field 'threshType'. The field 'threshType' has the - * following description: loosely specified enumeration: NONE,ABOVE, or BELOW + * Returns the value of field 'threshType'. * * @return the value of field 'ThreshType'. */ - public java.lang.String getThreshType() + public jalview.binding.types.ColourThreshTypeType getThreshType() { return this._threshType; } @@ -370,6 +484,76 @@ public class Colour 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 @@ -429,7 +613,9 @@ public class Colour implements java.io.Serializable } /** - * Sets the value of field 'name'. + * Sets the value of field 'name'. The field 'name' has the following + * description: Single letter residue code for an alignment colour scheme, or + * feature type for a feature colour scheme * * @param name * the value of field 'name'. @@ -440,6 +626,18 @@ public class Colour implements java.io.Serializable } /** + * Sets the value of field 'noValueColour'. + * + * @param noValueColour + * the value of field 'noValueColour'. + */ + public void setNoValueColour( + final jalview.binding.types.NoValueColour noValueColour) + { + this._noValueColour = noValueColour; + } + + /** * Sets the value of field 'RGB'. * * @param RGB @@ -451,13 +649,13 @@ public class Colour implements java.io.Serializable } /** - * Sets the value of field 'threshType'. The field 'threshType' has the - * following description: loosely specified enumeration: NONE,ABOVE, or BELOW + * Sets the value of field 'threshType'. * * @param threshType * the value of field 'threshType'. */ - public void setThreshType(final java.lang.String threshType) + public void setThreshType( + final jalview.binding.types.ColourThreshTypeType threshType) { this._threshType = threshType; } @@ -485,12 +683,13 @@ public class Colour implements java.io.Serializable * if this object is an invalid instance according to the schema * @return the unmarshaled jalview.binding.Colour */ - public static jalview.binding.Colour unmarshal(final java.io.Reader reader) + public static jalview.binding.Colour unmarshal( + final java.io.Reader reader) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.binding.Colour) Unmarshaller.unmarshal( - jalview.binding.Colour.class, reader); + return (jalview.binding.Colour) Unmarshaller + .unmarshal(jalview.binding.Colour.class, reader); } /**