X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FSetting.java;h=9a49315d219f7ec3c72091bb558b2a7e36a8124b;hb=6b71746c98f7c1118b474b0b920db3bd7b2a15c0;hp=56c3fe656315530eb684a9363a6ff2713487f2f6;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/schemabinding/version2/Setting.java b/src/jalview/schemabinding/version2/Setting.java index 56c3fe6..9a49315 100755 --- a/src/jalview/schemabinding/version2/Setting.java +++ b/src/jalview/schemabinding/version2/Setting.java @@ -1,26 +1,25 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) + * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle * - * This program 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 2 - * of the License, or (at your option) any later version. + * This file is part of Jalview. * - * This program 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. + * 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. * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * 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 . */ package jalview.schemabinding.version2; -// ---------------------------------/ -// - Imported classes and packages -/ -// ---------------------------------/ +//---------------------------------/ +//- Imported classes and packages -/ +//---------------------------------/ import org.exolab.castor.xml.Marshaller; import org.exolab.castor.xml.Unmarshaller; @@ -72,6 +71,76 @@ public class Setting implements java.io.Serializable */ private boolean _has_order; + /** + * Optional minimum colour for graduated feature colour + */ + private int _mincolour; + + /** + * keeps track of state for field: _mincolour + */ + private boolean _has_mincolour; + + /** + * threshold value for graduated feature colour + */ + private float _threshold; + + /** + * keeps track of state for field: _threshold + */ + private boolean _has_threshold; + + /** + * threshold type for graduated feature colour + */ + private int _threshstate; + + /** + * keeps track of state for field: _threshstate + */ + private boolean _has_threshstate; + + /** + * Field _max. + */ + private float _max; + + /** + * keeps track of state for field: _max + */ + private boolean _has_max; + + /** + * Field _min. + */ + private float _min; + + /** + * keeps track of state for field: _min + */ + private boolean _has_min; + + /** + * Field _colourByLabel. + */ + private boolean _colourByLabel; + + /** + * keeps track of state for field: _colourByLabel + */ + private boolean _has_colourByLabel; + + /** + * Field _autoScale. + */ + private boolean _autoScale; + + /** + * keeps track of state for field: _autoScale + */ + private boolean _has_autoScale; + // ----------------/ // - Constructors -/ // ----------------/ @@ -86,27 +155,86 @@ public class Setting implements java.io.Serializable // -----------/ /** - */ + */ + 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; + } + + /** + * Returns the value of field 'autoScale'. + * + * @return the value of field 'AutoScale'. + */ + public boolean getAutoScale() + { + return this._autoScale; + } + + /** * Returns the value of field 'colour'. * * @return the value of field 'Colour'. @@ -117,6 +245,16 @@ public class Setting implements java.io.Serializable } /** + * Returns the value of field 'colourByLabel'. + * + * @return the value of field 'ColourByLabel'. + */ + public boolean getColourByLabel() + { + return this._colourByLabel; + } + + /** * Returns the value of field 'display'. * * @return the value of field 'Display'. @@ -127,6 +265,37 @@ public class Setting implements java.io.Serializable } /** + * Returns the value of field 'max'. + * + * @return the value of field 'Max'. + */ + public float getMax() + { + return this._max; + } + + /** + * Returns the value of field 'min'. + * + * @return the value of field 'Min'. + */ + public float getMin() + { + return this._min; + } + + /** + * Returns the value of field 'mincolour'. The field 'mincolour' has the + * following description: Optional minimum colour for graduated feature colour + * + * @return the value of field 'Mincolour'. + */ + public int getMincolour() + { + return this._mincolour; + } + + /** * Returns the value of field 'order'. * * @return the value of field 'Order'. @@ -137,6 +306,28 @@ public class Setting implements java.io.Serializable } /** + * Returns the value of field 'threshold'. The field 'threshold' has the + * following description: threshold value for graduated feature colour + * + * @return the value of field 'Threshold'. + */ + public float getThreshold() + { + return this._threshold; + } + + /** + * Returns the value of field 'threshstate'. The field 'threshstate' has the + * following description: threshold type for graduated feature colour + * + * @return the value of field 'Threshstate'. + */ + public int getThreshstate() + { + return this._threshstate; + } + + /** * Returns the value of field 'type'. * * @return the value of field 'Type'. @@ -147,6 +338,16 @@ public class Setting implements java.io.Serializable } /** + * Method hasAutoScale. + * + * @return true if at least one AutoScale has been added + */ + public boolean hasAutoScale() + { + return this._has_autoScale; + } + + /** * Method hasColour. * * @return true if at least one Colour has been added @@ -157,6 +358,16 @@ public class Setting implements java.io.Serializable } /** + * Method hasColourByLabel. + * + * @return true if at least one ColourByLabel has been added + */ + public boolean hasColourByLabel() + { + return this._has_colourByLabel; + } + + /** * Method hasDisplay. * * @return true if at least one Display has been added @@ -167,6 +378,36 @@ public class Setting implements java.io.Serializable } /** + * Method hasMax. + * + * @return true if at least one Max has been added + */ + public boolean hasMax() + { + return this._has_max; + } + + /** + * Method hasMin. + * + * @return true if at least one Min has been added + */ + public boolean hasMin() + { + return this._has_min; + } + + /** + * Method hasMincolour. + * + * @return true if at least one Mincolour has been added + */ + public boolean hasMincolour() + { + return this._has_mincolour; + } + + /** * Method hasOrder. * * @return true if at least one Order has been added @@ -177,6 +418,46 @@ public class Setting implements java.io.Serializable } /** + * Method hasThreshold. + * + * @return true if at least one Threshold has been added + */ + public boolean hasThreshold() + { + return this._has_threshold; + } + + /** + * Method hasThreshstate. + * + * @return true if at least one Threshstate has been added + */ + public boolean hasThreshstate() + { + return this._has_threshstate; + } + + /** + * Returns the value of field 'autoScale'. + * + * @return the value of field 'AutoScale'. + */ + public boolean isAutoScale() + { + return this._autoScale; + } + + /** + * Returns the value of field 'colourByLabel'. + * + * @return the value of field 'ColourByLabel'. + */ + public boolean isColourByLabel() + { + return this._colourByLabel; + } + + /** * Returns the value of field 'display'. * * @return the value of field 'Display'. @@ -208,11 +489,10 @@ public class Setting implements java.io.Serializable * * @param out * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling + * if object is null or if any SAXException is thrown during + * marshaling * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the - * schema + * if this object is an invalid instance according to the schema */ public void marshal(final java.io.Writer out) throws org.exolab.castor.xml.MarshalException, @@ -226,13 +506,12 @@ public class Setting implements java.io.Serializable * * @param handler * @throws java.io.IOException - * if an IOException occurs during marshaling + * if an IOException occurs during marshaling * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the - * schema + * if this object is an invalid instance according to the schema * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling + * if object is null or if any SAXException is thrown during + * marshaling */ public void marshal(final org.xml.sax.ContentHandler handler) throws java.io.IOException, @@ -243,10 +522,22 @@ public class Setting implements java.io.Serializable } /** + * Sets the value of field 'autoScale'. + * + * @param autoScale + * the value of field 'autoScale'. + */ + public void setAutoScale(final boolean autoScale) + { + this._autoScale = autoScale; + this._has_autoScale = true; + } + + /** * Sets the value of field 'colour'. * * @param colour - * the value of field 'colour'. + * the value of field 'colour'. */ public void setColour(final int colour) { @@ -255,10 +546,22 @@ public class Setting implements java.io.Serializable } /** + * Sets the value of field 'colourByLabel'. + * + * @param colourByLabel + * the value of field 'colourByLabel'. + */ + public void setColourByLabel(final boolean colourByLabel) + { + this._colourByLabel = colourByLabel; + this._has_colourByLabel = true; + } + + /** * Sets the value of field 'display'. * * @param display - * the value of field 'display'. + * the value of field 'display'. */ public void setDisplay(final boolean display) { @@ -267,10 +570,47 @@ public class Setting implements java.io.Serializable } /** + * Sets the value of field 'max'. + * + * @param max + * the value of field 'max'. + */ + public void setMax(final float max) + { + this._max = max; + this._has_max = true; + } + + /** + * Sets the value of field 'min'. + * + * @param min + * the value of field 'min'. + */ + public void setMin(final float min) + { + this._min = min; + this._has_min = true; + } + + /** + * Sets the value of field 'mincolour'. The field 'mincolour' has the + * following description: Optional minimum colour for graduated feature colour + * + * @param mincolour + * the value of field 'mincolour'. + */ + public void setMincolour(final int mincolour) + { + this._mincolour = mincolour; + this._has_mincolour = true; + } + + /** * Sets the value of field 'order'. * * @param order - * the value of field 'order'. + * the value of field 'order'. */ public void setOrder(final float order) { @@ -279,10 +619,36 @@ public class Setting implements java.io.Serializable } /** + * Sets the value of field 'threshold'. The field 'threshold' has the + * following description: threshold value for graduated feature colour + * + * @param threshold + * the value of field 'threshold'. + */ + public void setThreshold(final float threshold) + { + this._threshold = threshold; + this._has_threshold = true; + } + + /** + * Sets the value of field 'threshstate'. The field 'threshstate' has the + * following description: threshold type for graduated feature colour + * + * @param threshstate + * the value of field 'threshstate'. + */ + public void setThreshstate(final int threshstate) + { + this._threshstate = threshstate; + this._has_threshstate = true; + } + + /** * Sets the value of field 'type'. * * @param type - * the value of field 'type'. + * the value of field 'type'. */ public void setType(final java.lang.String type) { @@ -294,11 +660,10 @@ public class Setting implements java.io.Serializable * * @param reader * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling + * if object is null or if any SAXException is thrown during + * marshaling * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the - * schema + * if this object is an invalid instance according to the schema * @return the unmarshaled jalview.schemabinding.version2.Settin */ public static jalview.schemabinding.version2.Setting unmarshal( @@ -314,8 +679,7 @@ public class Setting implements java.io.Serializable * * * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the - * schema + * if this object is an invalid instance according to the schema */ public void validate() throws org.exolab.castor.xml.ValidationException {