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Coverage Report

  1. Project Clover database Wed Nov 13 2024 16:12:26 GMT
  2. Package jalview.appletgui

File SplitFrame.java

 

Coverage histogram

../../img/srcFileCovDistChart0.png
59% of files have more coverage

Code metrics

32
68
8
1
238
137
25
0.37
8.5
8
3.12

Classes

Class Line # Actions
SplitFrame 35 68 25
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.appletgui;
22   
23    import jalview.api.AlignmentViewPanel;
24    import jalview.api.ViewStyleI;
25    import jalview.bin.JalviewLite;
26    import jalview.datamodel.AlignmentI;
27    import jalview.structure.StructureSelectionManager;
28    import jalview.viewmodel.AlignmentViewport;
29   
30    import java.awt.BorderLayout;
31    import java.awt.Dimension;
32    import java.awt.GridLayout;
33    import java.awt.Panel;
34   
 
35    public class SplitFrame extends EmbmenuFrame
36    {
37    private static final long serialVersionUID = 1L;
38   
39    private AlignFrame topFrame;
40   
41    private AlignFrame bottomFrame;
42   
43    private Panel outermost;
44   
45    /**
46    * Constructs the split frame placing cdna in the top half. No 'alignment' is
47    * performed here, this should be done by the calling client if wanted.
48    */
 
49  0 toggle public SplitFrame(AlignFrame af1, AlignFrame af2)
50    {
51  0 boolean af1IsNucleotide = af1.viewport.getAlignment().isNucleotide();
52  0 topFrame = af1IsNucleotide ? af1 : af2;
53  0 bottomFrame = topFrame == af1 ? af2 : af1;
54  0 init();
55    }
56   
57    /**
58    * Creates a Panel containing two Panels, and adds the first and second
59    * AlignFrame's components to each. At this stage we have not yet committed to
60    * whether the enclosing panel will be added to this frame, for display as a
61    * separate frame, or added to the applet (embedded mode).
62    */
 
63  0 toggle public void init()
64    {
65  0 constructSplit();
66   
67    /*
68    * Try to make and add dna/protein sequence mappings
69    */
70  0 final AlignViewport topViewport = topFrame.viewport;
71  0 final AlignViewport bottomViewport = bottomFrame.viewport;
72  0 final AlignmentI topAlignment = topViewport.getAlignment();
73  0 final AlignmentI bottomAlignment = bottomViewport.getAlignment();
74  0 AlignmentViewport cdna = topAlignment.isNucleotide() ? topViewport
75  0 : (bottomAlignment.isNucleotide() ? bottomViewport : null);
76  0 AlignmentViewport protein = !topAlignment.isNucleotide() ? topViewport
77  0 : (!bottomAlignment.isNucleotide() ? bottomViewport : null);
78   
79  0 final StructureSelectionManager ssm = StructureSelectionManager
80    .getStructureSelectionManager(topViewport.applet);
81  0 ssm.registerMappings(protein.getAlignment().getCodonFrames());
82  0 topViewport.setCodingComplement(bottomViewport);
83  0 ssm.addCommandListener(cdna);
84  0 ssm.addCommandListener(protein);
85   
86    /*
87    * Compute cDNA consensus on protein alignment
88    */
89  0 protein.initComplementConsensus();
90  0 AlignmentViewPanel ap = topAlignment.isNucleotide()
91    ? bottomFrame.alignPanel
92    : topFrame.alignPanel;
93  0 protein.updateConsensus(ap);
94   
95  0 adjustLayout();
96    }
97   
98    /**
99    *
100    */
 
101  0 toggle protected void constructSplit()
102    {
103  0 setMenuBar(null);
104  0 outermost = new Panel(new GridLayout(2, 1));
105   
106  0 Panel topPanel = new Panel();
107  0 Panel bottomPanel = new Panel();
108  0 outermost.add(topPanel);
109  0 outermost.add(bottomPanel);
110   
111  0 addAlignFrameComponents(topFrame, topPanel);
112  0 addAlignFrameComponents(bottomFrame, bottomPanel);
113    }
114   
115    /**
116    * Make any adjustments to the layout
117    */
 
118  0 toggle protected void adjustLayout()
119    {
120  0 AlignmentViewport cdna = topFrame.getAlignViewport().getAlignment()
121    .isNucleotide() ? topFrame.viewport : bottomFrame.viewport;
122  0 AlignmentViewport protein = cdna == topFrame.viewport
123    ? bottomFrame.viewport
124    : topFrame.viewport;
125   
126    /*
127    * Ensure sequence ids are the same width for good alignment.
128    */
129    // TODO should do this via av.getViewStyle/setViewStyle
130    // however at present av.viewStyle is not set in IdPanel.fontChanged
131  0 int w1 = topFrame.alignPanel.idPanel.idCanvas.getWidth();
132  0 int w2 = bottomFrame.alignPanel.idPanel.idCanvas.getWidth();
133  0 int w3 = Math.max(w1, w2);
134  0 if (w1 != w3)
135    {
136  0 Dimension d = topFrame.alignPanel.idPanel.idCanvas.getSize();
137  0 topFrame.alignPanel.idPanel.idCanvas
138    .setSize(new Dimension(w3, d.height));
139    }
140  0 if (w2 != w3)
141    {
142  0 Dimension d = bottomFrame.alignPanel.idPanel.idCanvas.getSize();
143  0 bottomFrame.alignPanel.idPanel.idCanvas
144    .setSize(new Dimension(w3, d.height));
145    }
146   
147    /*
148    * Scale protein to either 1 or 3 times character width of dna
149    */
150  0 if (protein != null && cdna != null)
151    {
152  0 ViewStyleI vs = protein.getViewStyle();
153  0 int scale = vs.isScaleProteinAsCdna() ? 3 : 1;
154  0 vs.setCharWidth(scale * cdna.getViewStyle().getCharWidth());
155  0 protein.setViewStyle(vs);
156    }
157    }
158   
159    /**
160    * Add the menu bar, alignment panel and status bar from the AlignFrame to the
161    * panel. The menu bar is a panel 'reconstructed' from the AlignFrame's frame
162    * menu bar. This allows each half of the SplitFrame to have its own menu bar.
163    *
164    * @param af
165    * @param panel
166    */
 
167  0 toggle private void addAlignFrameComponents(AlignFrame af, Panel panel)
168    {
169  0 panel.setLayout(new BorderLayout());
170  0 Panel menuPanel = af.makeEmbeddedPopupMenu(af.getMenuBar(), true,
171    false);
172  0 panel.add(menuPanel, BorderLayout.NORTH);
173  0 panel.add(af.statusBar, BorderLayout.SOUTH);
174  0 panel.add(af.alignPanel, BorderLayout.CENTER);
175   
176  0 af.setSplitFrame(this);
177    }
178   
179    /**
180    * Display the content panel either as a new frame or embedded in the applet.
181    *
182    * @param embedded
183    * @param applet
184    */
 
185  0 toggle public void addToDisplay(boolean embedded, JalviewLite applet)
186    {
187  0 createSplitFrameWindow(embedded, applet);
188  0 validate();
189  0 topFrame.alignPanel.adjustAnnotationHeight();
190  0 topFrame.alignPanel.paintAlignment(true, true);
191  0 bottomFrame.alignPanel.adjustAnnotationHeight();
192  0 bottomFrame.alignPanel.paintAlignment(true, true);
193    }
194   
195    /**
196    * Either show the content panel in this frame as a new frame, or (if
197    * embed=true) add it to the applet container instead.
198    *
199    * @param embed
200    * @param applet
201    */
 
202  0 toggle protected void createSplitFrameWindow(boolean embed, JalviewLite applet)
203    {
204  0 if (embed)
205    {
206  0 applet.add(outermost);
207  0 applet.validate();
208    }
209    else
210    {
211  0 this.add(outermost);
212  0 int width = Math.max(topFrame.frameWidth, bottomFrame.frameWidth);
213  0 int height = topFrame.frameHeight + bottomFrame.frameHeight;
214  0 jalview.bin.JalviewLite.addFrame(this, this.getTitle(), width,
215    height);
216    }
217    }
218   
219    /**
220    * Returns the contained AlignFrame complementary to the one given (or null if
221    * no match to top or bottom component).
222    *
223    * @param af
224    * @return
225    */
 
226  0 toggle public AlignFrame getComplement(AlignFrame af)
227    {
228  0 if (topFrame == af)
229    {
230  0 return bottomFrame;
231    }
232  0 else if (bottomFrame == af)
233    {
234  0 return topFrame;
235    }
236  0 return null;
237    }
238    }