Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AlignmentAnnotationFactory	45	12	7	0.00%	Show methods

Class AlignmentAnnotationFactory

Class AlignmentAnnotationFactory	Line # 45	Total Statements 12	Complexity 7	TOTAL Coverage 0.00%
newCalculator(FeatureSetCounterI) : void   newCalculator(FeatureSetCounterI) : void	5353	5.05	2.02	0.0 0.00%
newCalculator(AnnotationProviderI) : void   newCalculator(AnnotationProviderI) : void	7373	4.04	2.02	0.0 0.00%
newCalculator(AlignViewportI,AlignmentViewPanel,AnnotationProviderI) : void   newCalculator(AlignViewportI,AlignmentViewPanel,AnnotationProviderI) : void	9999	1.01	1.01	0.0 0.00%
newAnnotation(String,String,char,float,Color) : Annotation   newAnnotation(String,String,char,float,Color) : Annotation	115115	1.01	1.01	0.0 0.00%
newAlignmentAnnotation(String,String,Annotation[]) : AlignmentAnnotation   newAlignmentAnnotation(String,String,Annotation[]) : AlignmentAnnotation	130130	1.01	1.01	0.0 0.00%

 

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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.workers;
22
23		import java.awt.Color;
24
25		import jalview.api.AlignViewportI;
26		import jalview.api.AlignmentViewPanel;
27		import jalview.bin.Jalview;
28		import jalview.datamodel.AlignmentAnnotation;
29		import jalview.datamodel.Annotation;
30		import jalview.gui.AlignFrame;
31
32		/**
33		* Factory class with methods which allow clients (including external scripts
34		* such as Groovy) to 'register and forget' an alignment annotation calculator.
35		* <br>
36		* Currently supports two flavours of calculator:
37		* <ul>
38		* <li>a simple 'feature counter' which counts any desired score derivable from
39		* residue value and any sequence features at each position of the
40		* alignment</li>
41		* <li>a 'general purpose' calculator which computes one or more complete
42		* AlignmentAnnotation objects</li>
43		* </ul>
44		*/
		0% Uncovered Elements: 21 (21) Complexity: 7 Complexity Density: 0.58
45		public class AlignmentAnnotationFactory
46		{
47		/**
48		* Constructs and registers a new alignment annotation worker
49		*
50		* @param counter
51		* provider of feature counts per alignment position
52		*/
		0% Uncovered Elements: 7 (7) Complexity: 2 Complexity Density: 0.4
53	0	public static void newCalculator(FeatureSetCounterI counter)...
54		{
55	0	AlignmentViewPanel currentAlignFrame = Jalview.getInstance()
56		.getCurrentAlignFrame().alignPanel;
57	0	if (currentAlignFrame == null)
58		{
59	0	jalview.bin.Console.errPrintln(
60		"Can't register calculator as no alignment window has focus");
61	0	return;
62		}
63	0	new ColumnCounterSetWorker(currentAlignFrame.getAlignViewport(),
64		currentAlignFrame, counter);
65		}
66
67		/**
68		* Constructs and registers a new alignment annotation worker
69		*
70		* @param calculator
71		* provider of AlignmentAnnotation for the alignment
72		*/
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
73	0	public static void newCalculator(AnnotationProviderI calculator)...
74		{
75		// TODO need an interface for AlignFrame by which to access
76		// its AlignViewportI and AlignmentViewPanel
77	0	AlignFrame currentAlignFrame = Jalview.getInstance()
78		.getCurrentAlignFrame();
79	0	if (currentAlignFrame != null)
80		{
81	0	new AnnotationWorker(currentAlignFrame.getViewport(),
82		currentAlignFrame.getAlignPanels().get(0), calculator);
83		}
84		else
85		{
86	0	jalview.bin.Console.errPrintln(
87		"Can't register calculator as no alignment window has focus");
88		}
89		}
90
91		/**
92		* Constructs and registers a new alignment annotation worker
93		*
94		* @param viewport
95		* @param panel
96		* @param calculator
97		* provider of AlignmentAnnotation for the alignment
98		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
99	0	public static void newCalculator(AlignViewportI viewport,...
100		AlignmentViewPanel panel, AnnotationProviderI calculator)
101		{
102	0	new AnnotationWorker(viewport, panel, calculator);
103		}
104
105		/**
106		* Factory method to construct an Annotation object
107		*
108		* @param displayChar
109		* @param desc
110		* @param secondaryStructure
111		* @param val
112		* @param color
113		* @return
114		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
115	0	public static Annotation newAnnotation(String displayChar, String desc,...
116		char secondaryStructure, float val, Color color)
117		{
118	0	return new Annotation(displayChar, desc, secondaryStructure, val,
119		color);
120		}
121
122		/**
123		* Factory method to construct an AlignmentAnnotation object
124		*
125		* @param name
126		* @param desc
127		* @param anns
128		* @return
129		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
130	0	public static AlignmentAnnotation newAlignmentAnnotation(String name,...
131		String desc, Annotation[] anns)
132		{
133	0	return new AlignmentAnnotation(name, desc, anns);
134		}
135		}