Check hiddenSequence before placing in tmp
[jalview.git] / src / jalview / gui / Jalview2XML_V1.java
1 /*\r
2  * Jalview - A Sequence Alignment Editor and Viewer\r
3  * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
4  *\r
5  * This program is free software; you can redistribute it and/or\r
6  * modify it under the terms of the GNU General Public License\r
7  * as published by the Free Software Foundation; either version 2\r
8  * of the License, or (at your option) any later version.\r
9  *\r
10  * This program is distributed in the hope that it will be useful,\r
11  * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
13  * GNU General Public License for more details.\r
14  *\r
15  * You should have received a copy of the GNU General Public License\r
16  * along with this program; if not, write to the Free Software\r
17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
18  */\r
19 package jalview.gui;\r
20 \r
21 import jalview.schemes.*;\r
22 \r
23 import jalview.gui.*;\r
24 \r
25 import java.io.*;\r
26 \r
27 import java.net.*;\r
28 \r
29 import java.util.*;\r
30 \r
31 import java.util.jar.*;\r
32 \r
33 import javax.swing.*;\r
34 \r
35 import org.exolab.castor.xml.*;\r
36 \r
37 import jalview.binding.*;\r
38 \r
39 \r
40 \r
41 \r
42 /**\r
43  * DOCUMENT ME!\r
44  *\r
45  * @author $author$\r
46  * @version $Revision$\r
47  */\r
48 public class Jalview2XML_V1\r
49 {\r
50    jalview.schemes.UserColourScheme GetUserColourScheme(\r
51         JalviewModelSequence jms, String id)\r
52     {\r
53         UserColours[] uc = jms.getUserColours();\r
54         UserColours colours = null;\r
55 \r
56         for (int i = 0; i < uc.length; i++)\r
57         {\r
58             if (uc[i].getId().equals(id))\r
59             {\r
60                 colours = uc[i];\r
61 \r
62                 break;\r
63             }\r
64         }\r
65 \r
66         int csize = colours.getUserColourScheme().getColourCount();\r
67         java.awt.Color[] newColours = new java.awt.Color[csize];\r
68 \r
69         for (int i = 0; i < csize; i++)\r
70         {\r
71             newColours[i] = new java.awt.Color(Integer.parseInt(\r
72                         colours.getUserColourScheme().getColour(i).getRGB(), 16));\r
73         }\r
74 \r
75         return new jalview.schemes.UserColourScheme(newColours);\r
76     }\r
77 \r
78     /**\r
79      * DOCUMENT ME!\r
80      *\r
81      * @param file DOCUMENT ME!\r
82      */\r
83     public AlignFrame LoadJalviewAlign(String file)\r
84     {\r
85 \r
86         jalview.gui.AlignFrame af = null;\r
87 \r
88         try\r
89         {\r
90             //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING\r
91             URL url = null;\r
92 \r
93             if (file.startsWith("http://"))\r
94             {\r
95                 url = new URL(file);\r
96             }\r
97 \r
98             JarInputStream jin = null;\r
99             JarEntry jarentry = null;\r
100             int entryCount = 1;\r
101 \r
102             do\r
103             {\r
104                 if (url != null)\r
105                 {\r
106                     jin = new JarInputStream(url.openStream());\r
107                 }\r
108                 else\r
109                 {\r
110                     jin = new JarInputStream(new FileInputStream(file));\r
111                 }\r
112 \r
113                 for (int i = 0; i < entryCount; i++)\r
114                 {\r
115                     jarentry = jin.getNextJarEntry();\r
116                   }\r
117 \r
118                   class NoDescIDResolver implements IDResolver\r
119                   {\r
120                     public Object resolve(String idref)\r
121                     {\r
122                       System.out.println(idref+" used");\r
123                       return null;\r
124                     }\r
125                   }\r
126 \r
127 \r
128                 if (jarentry != null)\r
129                 {\r
130                     InputStreamReader in = new InputStreamReader(jin, "UTF-8");\r
131                     JalviewModel object = new JalviewModel();\r
132 \r
133                     object = (JalviewModel) object.unmarshal(in);\r
134 \r
135                     af = LoadFromObject(object);\r
136                     entryCount++;\r
137                 }\r
138             }\r
139             while (jarentry != null);\r
140         }\r
141         catch(java.net.UnknownHostException ex)\r
142         {\r
143           ex.printStackTrace();\r
144           System.err.println("Couldn't locate Jalview XML file : " +\r
145               ex + "\n");\r
146            JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
147                                     "Couldn't locate " + file,\r
148                                     "URL not found",\r
149                                     JOptionPane.WARNING_MESSAGE);\r
150 \r
151         }\r
152         catch (Exception ex)\r
153         {\r
154           ex.printStackTrace();\r
155             System.err.println("Exception whilst loading jalview XML file : " +\r
156                 ex + "\n");\r
157              JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
158                                       "Error loading  " + file,\r
159                                       "Error loading Jalview file",\r
160                                       JOptionPane.WARNING_MESSAGE);\r
161 \r
162         }\r
163 \r
164         return af;\r
165     }\r
166 \r
167     AlignFrame LoadFromObject(JalviewModel object)\r
168     {\r
169         Vector seqids = new Vector();\r
170         SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);\r
171         Sequence[] vamsasSeq = vamsasSet.getSequence();\r
172 \r
173         JalviewModelSequence jms = object.getJalviewModelSequence();\r
174 \r
175         //////////////////////////////////\r
176         //LOAD SEQUENCES\r
177         jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];\r
178         JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();\r
179         for (int i = 0; i < vamsasSeq.length; i++)\r
180         {\r
181             jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),\r
182                     vamsasSeq[i].getSequence());\r
183             jseqs[i].setStart(JSEQ[i].getStart());\r
184             jseqs[i].setEnd(JSEQ[i].getEnd());\r
185             jseqs[i].setColor(new java.awt.Color(JSEQ[i].getColour()));\r
186             seqids.add(jseqs[i]);\r
187         }\r
188 \r
189         ///SequenceFeatures are added to the DatasetSequence,\r
190         // so we must create the dataset before loading features\r
191         /////////////////////////////////\r
192         jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);\r
193         al.setDataset(null);\r
194         /////////////////////////////////\r
195 \r
196         for (int i = 0; i < vamsasSeq.length; i++)\r
197         {\r
198           if (JSEQ[i].getFeaturesCount() > 0)\r
199           {\r
200             Features[] features = JSEQ[i].getFeatures();\r
201             for (int f = 0; f < features.length; f++)\r
202             {\r
203               jalview.datamodel.SequenceFeature sf\r
204                   = new jalview.datamodel.SequenceFeature(features[f].getType(),\r
205                   features[f].getDescription(), features[f].getStatus(),\r
206                   features[f].getBegin(), features[f].getEnd(),\r
207                   null);\r
208 \r
209               al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);\r
210             }\r
211           }\r
212           if (JSEQ[i].getPdbidsCount() > 0)\r
213           {\r
214             Pdbids[] ids = JSEQ[i].getPdbids();\r
215             for (int p = 0; p < ids.length; p++)\r
216             {\r
217               jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();\r
218               entry.setId(ids[p].getId());\r
219               entry.setType(ids[p].getType());\r
220               al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);\r
221             }\r
222 \r
223           }\r
224         }\r
225 \r
226          /////////////////////////////////\r
227         //////////////////////////////////\r
228         //LOAD ANNOTATIONS\r
229         if (vamsasSet.getAnnotation() != null)\r
230         {\r
231             Annotation[] an = vamsasSet.getAnnotation();\r
232 \r
233             for (int i = 0; i < an.length; i++)\r
234             {\r
235                 AnnotationElement[] ae = an[i].getAnnotationElement();\r
236                 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];\r
237 \r
238                 for (int aa = 0; aa < ae.length; aa++)\r
239                 {\r
240                     anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),\r
241                             ae[aa].getDescription(),\r
242                             ae[aa].getSecondaryStructure().charAt(0),\r
243                             ae[aa].getValue());\r
244                 }\r
245 \r
246                 jalview.datamodel.AlignmentAnnotation jaa = null;\r
247 \r
248                 if (an[i].getGraph())\r
249                 {\r
250                     jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
251                             an[i].getDescription(), anot, 0, 0,\r
252                             jalview.datamodel.AlignmentAnnotation.BAR_GRAPH);\r
253                 }\r
254                 else\r
255                 {\r
256                     jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
257                             an[i].getDescription(), anot);\r
258                 }\r
259 \r
260                 al.addAnnotation(jaa);\r
261             }\r
262         }\r
263 \r
264 \r
265         /////////////////////////////////\r
266         // LOAD VIEWPORT\r
267         Viewport[] views = jms.getViewport();\r
268         Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER\r
269 \r
270         AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());\r
271 \r
272 \r
273         //  af.changeColour() );\r
274         /////////////////////////\r
275         //LOAD GROUPS\r
276         if (jms.getJGroupCount() > 0)\r
277         {\r
278             JGroup[] groups = jms.getJGroup();\r
279 \r
280             for (int i = 0; i < groups.length; i++)\r
281             {\r
282                 ColourSchemeI cs = null;\r
283 \r
284                 if (groups[i].getColour() != null)\r
285                 {\r
286                     if (groups[i].getColour().startsWith("ucs"))\r
287                     {\r
288                         cs = GetUserColourScheme(jms, groups[i].getColour());\r
289                     }\r
290                     else\r
291                     {\r
292                         cs = ColourSchemeProperty.getColour(al,\r
293                                 groups[i].getColour());\r
294                     }\r
295 \r
296                     if(cs!=null)\r
297                       cs.setThreshold(groups[i].getPidThreshold(), true);\r
298 \r
299                 }\r
300 \r
301                 Vector seqs = new Vector();\r
302                 int[] ids = groups[i].getSeq();\r
303 \r
304                 for (int s = 0; s < ids.length; s++)\r
305                 {\r
306                     seqs.addElement((jalview.datamodel.SequenceI) seqids.elementAt(\r
307                             ids[s]));\r
308                 }\r
309 \r
310                 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,\r
311                         groups[i].getName(), cs, groups[i].getDisplayBoxes(),\r
312                         groups[i].getDisplayText(), groups[i].getColourText(),\r
313                         groups[i].getStart(), groups[i].getEnd());\r
314 \r
315                 sg.setOutlineColour(new java.awt.Color(\r
316                         groups[i].getOutlineColour()));\r
317 \r
318                 if (groups[i].getConsThreshold() != 0)\r
319                 {\r
320                     jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",\r
321                             ResidueProperties.propHash, 3, sg.getSequences(false), 0,\r
322                             sg.getWidth() - 1);\r
323                     c.calculate();\r
324                     c.verdict(false, 25);\r
325                     sg.cs.setConservation(c);\r
326                 }\r
327 \r
328                 al.addGroup(sg);\r
329             }\r
330         }\r
331 \r
332 \r
333 \r
334         af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),\r
335             view.getHeight());\r
336         af.viewport.setStartRes(view.getStartRes());\r
337         af.viewport.setStartSeq(view.getStartSeq());\r
338         af.viewport.setShowAnnotation(view.getShowAnnotation());\r
339         af.viewport.setAbovePIDThreshold(view.getPidSelected());\r
340         af.abovePIDThreshold.setSelected(view.getPidSelected());\r
341         af.viewport.setColourText(view.getShowColourText());\r
342         af.colourTextMenuItem.setSelected(view.getShowColourText());\r
343         af.viewport.setConservationSelected(view.getConservationSelected());\r
344         af.conservationMenuItem.setSelected(view.getConservationSelected());\r
345 \r
346         af.viewport.setShowJVSuffix(view.getShowFullId());\r
347         af.seqLimits.setSelected(view.getShowFullId());\r
348 \r
349         af.viewport.setFont(new java.awt.Font(view.getFontName(),\r
350                 view.getFontStyle(), view.getFontSize()));\r
351         af.alignPanel.fontChanged();\r
352 \r
353         af.viewport.setRenderGaps(view.getRenderGaps());\r
354         af.renderGapsMenuItem.setSelected(view.getRenderGaps());\r
355 \r
356         af.viewport.setWrapAlignment(view.getWrapAlignment());\r
357         af.wrapMenuItem.setSelected(view.getWrapAlignment());\r
358 \r
359 \r
360         af.alignPanel.setWrapAlignment(view.getWrapAlignment());\r
361 \r
362         af.annotationPanelMenuItem.setState(view.getShowAnnotation());\r
363         af.viewport.setShowAnnotation(view.getShowAnnotation());\r
364         af.alignPanel.setAnnotationVisible(view.getShowAnnotation());\r
365 \r
366 \r
367         af.viewport.setShowBoxes(view.getShowBoxes());\r
368         af.viewBoxesMenuItem.setSelected(view.getShowBoxes());\r
369         af.viewport.setShowText(view.getShowText());\r
370         af.viewTextMenuItem.setSelected(view.getShowText());\r
371 \r
372         ColourSchemeI cs = null;\r
373 \r
374         if (view.getBgColour() != null)\r
375         {\r
376             if (view.getBgColour().startsWith("ucs"))\r
377             {\r
378                 cs = GetUserColourScheme(jms, view.getBgColour());\r
379             }\r
380             else\r
381             {\r
382                 cs = ColourSchemeProperty.getColour(al, view.getBgColour());\r
383             }\r
384 \r
385             if(cs!=null)\r
386             {\r
387               cs.setThreshold(view.getPidThreshold(), true);\r
388               cs.setConsensus(af.viewport.hconsensus);\r
389             }\r
390         }\r
391 \r
392         af.setColourSelected(view.getBgColour());\r
393         af.viewport.setGlobalColourScheme(cs);\r
394         af.viewport.setColourAppliesToAllGroups(false);\r
395         af.changeColour(cs);\r
396         if (view.getConservationSelected() && cs!=null)\r
397         {\r
398           cs.setConservationInc(view.getConsThreshold());\r
399         }\r
400 \r
401         af.viewport.setColourAppliesToAllGroups(true);\r
402 \r
403         if (view.getShowSequenceFeatures())\r
404         {\r
405            af.viewport.showSequenceFeatures = true;\r
406            af.showSeqFeatures.setSelected(true);\r
407         }\r
408 \r
409         if(jms.getFeatureSettings()!=null)\r
410         {\r
411           af.viewport.featuresDisplayed = new Hashtable();\r
412           String [] renderOrder = new String[jms.getFeatureSettings().getSettingCount()];\r
413          for(int fs=0; fs<jms.getFeatureSettings().getSettingCount(); fs++)\r
414          {\r
415            Setting setting = jms.getFeatureSettings().getSetting(fs);\r
416 \r
417            af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),\r
418                new java.awt.Color(setting.getColour()));\r
419 \r
420            renderOrder[fs] = setting.getType();\r
421 \r
422            if(setting.getDisplay())\r
423              af.viewport.featuresDisplayed.put(\r
424                  setting.getType(), new Integer(setting.getColour()));\r
425          }\r
426          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;\r
427         }\r
428 \r
429 \r
430         Desktop.addInternalFrame(af, view.getTitle(),\r
431              view.getWidth(), view.getHeight());\r
432 \r
433         //LOAD TREES\r
434         ///////////////////////////////////////\r
435         if (jms.getTreeCount() > 0)\r
436         {\r
437             try\r
438             {\r
439                 for (int t = 0; t < jms.getTreeCount(); t++)\r
440                 {\r
441 \r
442                     Tree tree = jms.getTree(t);\r
443 \r
444                     TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(\r
445                                 tree.getNewick()), tree.getTitle(),\r
446                                 tree.getWidth(), tree.getHeight(),\r
447                                 tree.getXpos(), tree.getYpos());\r
448 \r
449                     tp.fitToWindow.setState(tree.getFitToWindow());\r
450                     tp.fitToWindow_actionPerformed(null);\r
451 \r
452                     if(tree.getFontName()!=null)\r
453                       tp.setTreeFont(new java.awt.Font(tree.getFontName(),\r
454                                           tree.getFontStyle(),\r
455                                           tree.getFontSize()));\r
456                     else\r
457                       tp.setTreeFont(new java.awt.Font(view.getFontName(),\r
458                                             view.getFontStyle(),\r
459                                             tree.getFontSize()));\r
460 \r
461                     tp.showPlaceholders(tree.getMarkUnlinked());\r
462                     tp.showBootstrap(tree.getShowBootstrap());\r
463                     tp.showDistances(tree.getShowDistances());\r
464 \r
465                     tp.treeCanvas.threshold = tree.getThreshold();\r
466 \r
467                     if (tree.getCurrentTree())\r
468                       af.viewport.setCurrentTree(tp.getTree());\r
469                 }\r
470 \r
471             }\r
472             catch (Exception ex)\r
473             {\r
474                 ex.printStackTrace();\r
475             }\r
476 \r
477         }\r
478 \r
479         return af;\r
480     }\r
481 }\r
482 \r