Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AnnotationRowFilter	36	39	20	0.00%	Show methods

Class AnnotationRowFilter

Class AnnotationRowFilter	Line # 36	Total Statements 39	Complexity 20	TOTAL Coverage 0.00%
AnnotationRowFilter(AlignViewport,AlignmentPanel)   AnnotationRowFilter(AlignViewport,AlignmentPanel)	7878	2.02	1.01	0.0 0.00%
AnnotationRowFilter()   AnnotationRowFilter()	8484	0.00	1.01	-1.0 -1.0 -
getSelectedThresholdItem(int) : int   getSelectedThresholdItem(int) : int	8989	6.06	3.03	0.0 0.00%
modelChanged() : void   modelChanged() : void	103103	1.01	1.01	0.0 0.00%
ok_actionPerformed(ActionEvent) : void   ok_actionPerformed(ActionEvent) : void	108108	2.02	1.01	0.0 0.00%
cancel_actionPerformed(ActionEvent) : void   cancel_actionPerformed(ActionEvent) : void	114114	3.03	1.01	0.0 0.00%
thresholdCheck_actionPerformed(ActionEvent) : void   thresholdCheck_actionPerformed(ActionEvent) : void	121121	1.01	1.01	0.0 0.00%
annotations_actionPerformed(ActionEvent) : void   annotations_actionPerformed(ActionEvent) : void	126126	1.01	1.01	0.0 0.00%
threshold_actionPerformed(ActionEvent) : void   threshold_actionPerformed(ActionEvent) : void	131131	1.01	1.01	0.0 0.00%
setThresholdValueText() : void   setThresholdValueText() : void	140140	9.09	2.02	0.0 0.00%
thresholdValue_actionPerformed(ActionEvent) : void   thresholdValue_actionPerformed(ActionEvent) : void	158158	7.07	3.03	0.0 0.00%
percentageValue_actionPerformed() : void   percentageValue_actionPerformed() : void	180180	1.01	1.01	0.0 0.00%
populateThresholdComboBox(Choice) : void   populateThresholdComboBox(Choice) : void	185185	3.03	1.01	0.0 0.00%
getCurrentAnnotation() : jalview.datamodel.AlignmentAnnotation   getCurrentAnnotation() : jalview.datamodel.AlignmentAnnotation	195195	1.01	1.01	0.0 0.00%
setCurrentAnnotation(jalview.datamodel.AlignmentAnnotation) : void   setCurrentAnnotation(jalview.datamodel.AlignmentAnnotation) : void	200200	1.01	1.01	0.0 0.00%

 

Contributing tests

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1		/*
2		* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3		* Copyright (C) $$Year-Rel$$ The Jalview Authors
4		*
5		* This file is part of Jalview.
6		*
7		* Jalview is free software: you can redistribute it and/or
8		* modify it under the terms of the GNU General Public License
9		* as published by the Free Software Foundation, either version 3
10		* of the License, or (at your option) any later version.
11		*
12		* Jalview is distributed in the hope that it will be useful, but
13		* WITHOUT ANY WARRANTY; without even the implied warranty
14		* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15		* PURPOSE. See the GNU General Public License for more details.
16		*
17		* You should have received a copy of the GNU General Public License
18		* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19		* The Jalview Authors are detailed in the 'AUTHORS' file.
20		*/
21		package jalview.appletgui;
22
23		import jalview.schemes.AnnotationColourGradient;
24		import jalview.util.MessageManager;
25
26		import java.awt.Button;
27		import java.awt.Checkbox;
28		import java.awt.Choice;
29		import java.awt.Frame;
30		import java.awt.Panel;
31		import java.awt.Scrollbar;
32		import java.awt.TextField;
33		import java.awt.event.ActionEvent;
34
35		@SuppressWarnings("serial")
		0% Uncovered Elements: 62 (62) Complexity: 20 Complexity Density: 0.51
36		public abstract class AnnotationRowFilter extends Panel
37		{
38		protected AlignViewport av;
39
40		protected AlignmentPanel ap;
41
42		protected int[] annmap;
43
44		protected boolean enableSeqAss = false;
45
46		private jalview.datamodel.AlignmentAnnotation currentAnnotation;
47
48		protected boolean adjusting = false;
49
50		protected Checkbox currentColours = new Checkbox();
51
52		protected Panel minColour = new Panel();
53
54		protected Panel maxColour = new Panel();
55
56		protected Checkbox seqAssociated = new Checkbox();
57
58		protected Checkbox thresholdIsMin = new Checkbox();
59
60		protected Scrollbar slider = new Scrollbar(Scrollbar.HORIZONTAL);
61
62		protected Checkbox percentThreshold = new Checkbox();
63
64		protected TextField thresholdValue = new TextField(20);
65
66		protected Frame frame;
67
68		protected Button ok = new Button();
69
70		protected Button cancel = new Button();
71
72		/**
73		* enabled if the user is dragging the slider - try to keep updates to a
74		* minimun
75		*/
76		protected boolean sliderDragging = false;
77
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
78	0	public AnnotationRowFilter(AlignViewport av, final AlignmentPanel ap)...
79		{
80	0	this.av = av;
81	0	this.ap = ap;
82		}
83
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
84	0	public AnnotationRowFilter()...
85		{
86
87		}
88
		0% Uncovered Elements: 10 (10) Complexity: 3 Complexity Density: 0.5
89	0	protected int getSelectedThresholdItem(int indexValue)...
90		{
91	0	int selectedThresholdItem = -1;
92	0	if (indexValue == 1)
93		{
94	0	selectedThresholdItem = AnnotationColourGradient.ABOVE_THRESHOLD;
95		}
96	0	else if (indexValue == 2)
97		{
98	0	selectedThresholdItem = AnnotationColourGradient.BELOW_THRESHOLD;
99		}
100	0	return selectedThresholdItem;
101		}
102
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
103	0	public void modelChanged()...
104		{
105	0	seqAssociated.setEnabled(enableSeqAss);
106		}
107
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
108	0	public void ok_actionPerformed(ActionEvent e)...
109		{
110	0	updateView();
111	0	frame.setVisible(false);
112		}
113
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
114	0	public void cancel_actionPerformed(ActionEvent e)...
115		{
116	0	reset();
117	0	ap.paintAlignment(true, true);
118	0	frame.setVisible(false);
119		}
120
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
121	0	public void thresholdCheck_actionPerformed(ActionEvent e)...
122		{
123	0	updateView();
124		}
125
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
126	0	public void annotations_actionPerformed(ActionEvent e)...
127		{
128	0	updateView();
129		}
130
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
131	0	public void threshold_actionPerformed(ActionEvent e)...
132		{
133	0	updateView();
134		}
135
136		/**
137		* update the text field from the threshold slider. preserves state of
138		* 'adjusting' so safe to call in init.
139		*/
		0% Uncovered Elements: 11 (11) Complexity: 2 Complexity Density: 0.22
140	0	protected void setThresholdValueText()...
141		{
142	0	boolean oldadj = adjusting;
143	0	adjusting = true;
144	0	if (percentThreshold.getState())
145		{
146	0	double scl = slider.getMaximum() - slider.getMinimum();
147	0	scl = (slider.getValue() - slider.getMinimum()) / scl;
148	0	thresholdValue.setText(100f * scl + "");
149		}
150		else
151		{
152	0	thresholdValue.setText((slider.getValue() / 1000f) + "");
153		}
154	0	thresholdValue.setCaretPosition(0);
155	0	adjusting = oldadj;
156		}
157
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.43
158	0	public void thresholdValue_actionPerformed(ActionEvent e)...
159		{
160	0	try
161		{
162	0	float f = Float.parseFloat(thresholdValue.getText());
163	0	if (percentThreshold.getState())
164		{
165	0	int pos = slider.getMinimum()
166		+ (int) ((slider.getMaximum() - slider.getMinimum()) * f
167		/ 100f);
168	0	slider.setValue(pos);
169		}
170		else
171		{
172	0	slider.setValue((int) (f * 1000));
173		}
174	0	valueChanged(false);
175		} catch (NumberFormatException ex)
176		{
177		}
178		}
179
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
180	0	protected void percentageValue_actionPerformed()...
181		{
182	0	setThresholdValueText();
183		}
184
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
185	0	protected void populateThresholdComboBox(Choice threshold)...
186		{
187	0	threshold.addItem(MessageManager
188		.getString("label.threshold_feature_no_threshold"));
189	0	threshold.addItem(MessageManager
190		.getString("label.threshold_feature_above_threshold"));
191	0	threshold.addItem(MessageManager
192		.getString("label.threshold_feature_below_threshold"));
193		}
194
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
195	0	public jalview.datamodel.AlignmentAnnotation getCurrentAnnotation()...
196		{
197	0	return currentAnnotation;
198		}
199
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
200	0	public void setCurrentAnnotation(...
201		jalview.datamodel.AlignmentAnnotation currentAnnotation)
202		{
203	0	this.currentAnnotation = currentAnnotation;
204		}
205
206		public abstract void valueChanged(boolean updateAllAnnotation);
207
208		public abstract void updateView();
209
210		public abstract void reset();
211		}