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Coverage Report

  1. Project Clover database Mon Nov 11 2024 17:27:16 GMT
  2. Package jalview.appletgui

File AlignViewport.java

 

Coverage histogram

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

Code metrics

50
98
18
1
421
289
46
0.47
5.44
18
2.56

Classes

Class Line # Actions
AlignViewport 44 98 46
0.00%
 

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No tests hitting this source file were found.

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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.AlignViewportI;
24    import jalview.api.FeatureSettingsModelI;
25    import jalview.bin.JalviewLite;
26    import jalview.commands.CommandI;
27    import jalview.datamodel.AlignmentI;
28    import jalview.datamodel.ColumnSelection;
29    import jalview.datamodel.HiddenColumns;
30    import jalview.datamodel.SearchResults;
31    import jalview.datamodel.SearchResultsI;
32    import jalview.datamodel.SequenceGroup;
33    import jalview.renderer.ResidueShader;
34    import jalview.schemes.ColourSchemeProperty;
35    import jalview.schemes.UserColourScheme;
36    import jalview.structure.SelectionSource;
37    import jalview.structure.StructureSelectionManager;
38    import jalview.structure.VamsasSource;
39    import jalview.viewmodel.AlignmentViewport;
40   
41    import java.awt.Font;
42    import java.awt.FontMetrics;
43   
 
44    public class AlignViewport extends AlignmentViewport
45    implements SelectionSource
46    {
47    boolean cursorMode = false;
48   
49    Font font = new Font("SansSerif", Font.PLAIN, 10);
50   
51    boolean validCharWidth = true;
52   
53    public jalview.bin.JalviewLite applet;
54   
55    private AnnotationColumnChooser annotationColumnSelectionState;
56   
 
57  0 toggle public AlignViewport(AlignmentI al, JalviewLite applet)
58    {
59  0 super(al);
60  0 calculator = new jalview.workers.AlignCalcManager();
61  0 this.applet = applet;
62   
63    // we always pad gaps
64  0 this.setPadGaps(true);
65   
66  0 if (applet != null)
67    {
68    // get the width and height scaling factors if they were specified
69  0 String param = applet.getParameter("widthScale");
70  0 if (param != null)
71    {
72  0 try
73    {
74  0 widthScale = Float.valueOf(param).floatValue();
75    } catch (Exception e)
76    {
77    }
78  0 if (widthScale <= 1.0)
79    {
80  0 jalview.bin.Console.errPrintln(
81    "Invalid alignment character width scaling factor ("
82    + widthScale + "). Ignoring.");
83  0 widthScale = 1;
84    }
85  0 if (JalviewLite.debug)
86    {
87  0 jalview.bin.Console.errPrintln(
88    "Alignment character width scaling factor is now "
89    + widthScale);
90    }
91    }
92  0 param = applet.getParameter("heightScale");
93  0 if (param != null)
94    {
95  0 try
96    {
97  0 heightScale = Float.valueOf(param).floatValue();
98    } catch (Exception e)
99    {
100    }
101  0 if (heightScale <= 1.0)
102    {
103  0 jalview.bin.Console.errPrintln(
104    "Invalid alignment character height scaling factor ("
105    + heightScale + "). Ignoring.");
106  0 heightScale = 1;
107    }
108  0 if (JalviewLite.debug)
109    {
110  0 jalview.bin.Console.errPrintln(
111    "Alignment character height scaling factor is now "
112    + heightScale);
113    }
114    }
115    }
116  0 setFont(font, true);
117   
118  0 if (applet != null)
119    {
120  0 setShowJVSuffix(
121    applet.getDefaultParameter("showFullId", getShowJVSuffix()));
122   
123  0 setShowAnnotation(applet.getDefaultParameter("showAnnotation",
124    isShowAnnotation()));
125   
126  0 showConservation = applet.getDefaultParameter("showConservation",
127    showConservation);
128   
129  0 showQuality = applet.getDefaultParameter("showQuality", showQuality);
130   
131  0 showConsensus = applet.getDefaultParameter("showConsensus",
132    showConsensus);
133   
134  0 showOccupancy = applet.getDefaultParameter("showOccupancy",
135    showOccupancy);
136   
137  0 setShowUnconserved(applet.getDefaultParameter("showUnconserved",
138    getShowUnconserved()));
139   
140  0 setScaleProteinAsCdna(applet.getDefaultParameter("scaleProteinAsCdna",
141    isScaleProteinAsCdna()));
142   
143  0 String param = applet.getParameter("upperCase");
144  0 if (param != null)
145    {
146  0 if (param.equalsIgnoreCase("bold"))
147    {
148  0 setUpperCasebold(true);
149    }
150    }
151  0 sortByTree = applet.getDefaultParameter("sortByTree", sortByTree);
152   
153  0 setFollowHighlight(applet.getDefaultParameter("automaticScrolling",
154    isFollowHighlight()));
155  0 followSelection = isFollowHighlight();
156   
157  0 showSequenceLogo = applet.getDefaultParameter("showSequenceLogo",
158    showSequenceLogo);
159   
160  0 normaliseSequenceLogo = applet.getDefaultParameter(
161    "normaliseSequenceLogo", applet.getDefaultParameter(
162    "normaliseLogo", normaliseSequenceLogo));
163   
164  0 showGroupConsensus = applet.getDefaultParameter("showGroupConsensus",
165    showGroupConsensus);
166   
167  0 showGroupConservation = applet.getDefaultParameter(
168    "showGroupConservation", showGroupConservation);
169   
170  0 showConsensusHistogram = applet.getDefaultParameter(
171    "showConsensusHistogram", showConsensusHistogram);
172   
173    }
174   
175  0 if (applet != null)
176    {
177  0 String colour = al.isNucleotide()
178    ? applet.getParameter("defaultColourNuc")
179    : applet.getParameter("defaultColourProt");
180  0 if (colour == null)
181    {
182  0 colour = applet.getParameter("defaultColour");
183    }
184  0 if (colour == null)
185    {
186  0 colour = applet.getParameter("userDefinedColour");
187  0 if (colour != null)
188    {
189  0 colour = "User Defined";
190    }
191    }
192   
193  0 if (colour != null)
194    {
195  0 residueShading = new ResidueShader(ColourSchemeProperty
196    .getColourScheme(this, alignment, colour));
197  0 if (residueShading != null)
198    {
199  0 residueShading.setConsensus(hconsensus);
200    }
201    }
202   
203  0 if (applet.getParameter("userDefinedColour") != null)
204    {
205  0 residueShading = new ResidueShader(new UserColourScheme(
206    applet.getParameter("userDefinedColour")));
207    }
208    }
209  0 initAutoAnnotation();
210   
211    }
212   
213    java.awt.Frame nullFrame;
214   
215    protected FeatureSettings featureSettings = null;
216   
217    private float heightScale = 1, widthScale = 1;
218   
219    /**
220    * {@inheritDoc}
221    */
 
222  0 toggle @Override
223    public void setFont(Font f, boolean setGrid)
224    {
225  0 font = f;
226  0 if (nullFrame == null)
227    {
228  0 nullFrame = new java.awt.Frame();
229  0 nullFrame.addNotify();
230    }
231   
232  0 if (setGrid)
233    {
234  0 FontMetrics fm = nullFrame.getGraphics().getFontMetrics(font);
235  0 setCharHeight((int) (heightScale * fm.getHeight()));
236  0 setCharWidth((int) (widthScale * fm.charWidth('M')));
237    }
238   
239  0 if (isUpperCasebold())
240    {
241  0 Font f2 = new Font(f.getName(), Font.BOLD, f.getSize());
242  0 FontMetrics fm = nullFrame.getGraphics().getFontMetrics(f2);
243  0 setCharWidth(
244    (int) (widthScale * (fm.stringWidth("MMMMMMMMMMM") / 10)));
245    }
246    }
247   
 
248  0 toggle public Font getFont()
249    {
250  0 return font;
251    }
252   
 
253  0 toggle public void resetSeqLimits(int height)
254    {
255  0 ranges.setEndSeq(height / getCharHeight() - 1); // BH 2019.04.18
256    }
257   
258    boolean centreColumnLabels;
259   
 
260  0 toggle public boolean getCentreColumnLabels()
261    {
262  0 return centreColumnLabels;
263    }
264   
265    public boolean followSelection = true;
266   
267    /**
268    * @return true if view selection should always follow the selections
269    * broadcast by other selection sources
270    */
 
271  0 toggle public boolean getFollowSelection()
272    {
273  0 return followSelection;
274    }
275   
 
276  0 toggle @Override
277    public void sendSelection()
278    {
279  0 getStructureSelectionManager().sendSelection(
280    new SequenceGroup(getSelectionGroup()),
281    new ColumnSelection(getColumnSelection()),
282    new HiddenColumns(getAlignment().getHiddenColumns()), this);
283    }
284   
285    /**
286    * Returns an instance of the StructureSelectionManager scoped to this applet
287    * instance.
288    *
289    * @return
290    */
 
291  0 toggle @Override
292    public StructureSelectionManager getStructureSelectionManager()
293    {
294  0 return jalview.structure.StructureSelectionManager
295    .getStructureSelectionManager(applet);
296    }
297   
 
298  0 toggle @Override
299    public boolean isNormaliseSequenceLogo()
300    {
301  0 return normaliseSequenceLogo;
302    }
303   
 
304  0 toggle public void setNormaliseSequenceLogo(boolean state)
305    {
306  0 normaliseSequenceLogo = state;
307    }
308   
309    /**
310    *
311    * @return true if alignment characters should be displayed
312    */
 
313  0 toggle @Override
314    public boolean isValidCharWidth()
315    {
316  0 return validCharWidth;
317    }
318   
 
319  0 toggle public AnnotationColumnChooser getAnnotationColumnSelectionState()
320    {
321  0 return annotationColumnSelectionState;
322    }
323   
 
324  0 toggle public void setAnnotationColumnSelectionState(
325    AnnotationColumnChooser annotationColumnSelectionState)
326    {
327  0 this.annotationColumnSelectionState = annotationColumnSelectionState;
328    }
329   
 
330  0 toggle @Override
331    public void mirrorCommand(CommandI command, boolean undo,
332    StructureSelectionManager ssm, VamsasSource source)
333    {
334    // TODO refactor so this can be pulled up to superclass or controller
335    /*
336    * Do nothing unless we are a 'complement' of the source. May replace this
337    * with direct calls not via SSM.
338    */
339  0 if (source instanceof AlignViewportI
340    && ((AlignViewportI) source).getCodingComplement() == this)
341    {
342    // ok to continue;
343    }
344    else
345    {
346  0 return;
347    }
348   
349  0 CommandI mappedCommand = ssm.mapCommand(command, undo, getAlignment(),
350    getGapCharacter());
351  0 if (mappedCommand != null)
352    {
353  0 mappedCommand.doCommand(null);
354  0 firePropertyChange("alignment", null, getAlignment().getSequences());
355   
356    // ap.scalePanelHolder.repaint();
357    // ap.repaint();
358    }
359    }
360   
 
361  0 toggle @Override
362    public VamsasSource getVamsasSource()
363    {
364  0 return this;
365    }
366   
367    /**
368    * If this viewport has a (Protein/cDNA) complement, then scroll the
369    * complementary alignment to match this one.
370    */
 
371  0 toggle public void scrollComplementaryAlignment(AlignmentPanel complementPanel)
372    {
373  0 if (complementPanel == null)
374    {
375  0 return;
376    }
377   
378    /*
379    * Populate a SearchResults object with the mapped location to scroll to. If
380    * there is no complement, or it is not following highlights, or no mapping
381    * is found, the result will be empty.
382    */
383  0 SearchResultsI sr = new SearchResults();
384  0 int seqOffset = findComplementScrollTarget(sr);
385  0 if (!sr.isEmpty())
386    {
387  0 complementPanel.setToScrollComplementPanel(false);
388  0 complementPanel.scrollToCentre(sr, seqOffset);
389  0 complementPanel.setToScrollComplementPanel(true);
390    }
391    }
392   
393    /**
394    * Applies the supplied feature settings descriptor to currently known
395    * features. This supports an 'initial configuration' of feature colouring
396    * based on a preset or user favourite. This may then be modified in the usual
397    * way using the Feature Settings dialogue. NOT IMPLEMENTED FOR APPLET
398    *
399    * @param featureSettings
400    */
 
401  0 toggle @Override
402    public void applyFeaturesStyle(FeatureSettingsModelI featureSettings)
403    {
404    // TODO implement for applet
405    }
406   
407    /**
408    * Merges the supplied feature settings descriptor with existing feature
409    * styles. This supports an 'initial configuration' of feature colouring based
410    * on a preset or user favourite. This may then be modified in the usual way
411    * using the Feature Settings dialogue. NOT IMPLEMENTED FOR APPLET
412    *
413    * @param featureSettings
414    */
 
415  0 toggle @Override
416    public void mergeFeaturesStyle(FeatureSettingsModelI featureSettings)
417    {
418    // TODO Auto-generated method stub
419   
420    }
421    }
  • Report generated by OpenClover v 4.4.1 on Mon Nov 11 2024 17:34:35 GMT using coverage data from Mon Nov 11 2024 17:34:16 GMT.
  • OpenClover is free and open-source software.