src/jalview/gui/CrossRefAction.java

   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.gui;
  22
  23 import jalview.analysis.AlignmentUtils;
  24 import jalview.analysis.CrossRef;
  25 import jalview.api.AlignmentViewPanel;
  26 import jalview.api.FeatureSettingsModelI;
  27 import jalview.bin.Cache;
  28 import jalview.datamodel.Alignment;
  29 import jalview.datamodel.AlignmentI;
  30 import jalview.datamodel.DBRefSource;
  31 import jalview.datamodel.SequenceI;
  32 import jalview.io.gff.SequenceOntologyI;
  33 import jalview.structure.StructureSelectionManager;
  34 import jalview.util.MessageManager;
  35 import jalview.ws.SequenceFetcher;
  36
  37 import java.util.ArrayList;
  38 import java.util.List;
  39
  40 import javax.swing.JOptionPane;
  41
  42 /**
  43  * Factory constructor and runnable for discovering and displaying
  44  * cross-references for a set of aligned sequences
  45  *
  46  * @author jprocter
  47  *
  48  */
  49 public class CrossRefAction implements Runnable
  50 {
  51   private AlignFrame alignFrame;
  52
  53   private SequenceI[] sel;
  54
  55   private boolean _odna;
  56
  57   private String source;
  58
  59   List<AlignmentViewPanel> xrefViews = new ArrayList<AlignmentViewPanel>();
  60
  61   public List<jalview.api.AlignmentViewPanel> getXrefViews()
  62   {
  63     return xrefViews;
  64   }
  65
  66   @Override
  67   public void run()
  68   {
  69     final long sttime = System.currentTimeMillis();
  70     alignFrame.setProgressBar(MessageManager.formatMessage(
  71             "status.searching_for_sequences_from", new Object[]
  72             { source }), sttime);
  73     try
  74     {
  75       AlignmentI alignment = alignFrame.getViewport().getAlignment();
  76       AlignmentI dataset = alignment.getDataset() == null ? alignment
  77               : alignment.getDataset();
  78       boolean dna = alignment.isNucleotide();
  79       if (_odna != dna)
  80       {
  81         System.err
  82                 .println("Conflict: showProducts for alignment originally "
  83                         + "thought to be " + (_odna ? "DNA" : "Protein")
  84                         + " now searching for " + (dna ? "DNA" : "Protein")
  85                         + " Context.");
  86       }
  87       AlignmentI xrefs = new CrossRef(sel, dataset)
  88               .findXrefSequences(source, dna);
  89       if (xrefs == null)
  90       {
  91         return;
  92       }
  93       /*
  94        * get display scheme (if any) to apply to features
  95        */
  96       FeatureSettingsModelI featureColourScheme = new SequenceFetcher()
  97               .getFeatureColourScheme(source);
  98
  99       AlignmentI xrefsAlignment = makeCrossReferencesAlignment(dataset,
 100               xrefs);
 101       if (!dna)
 102       {
 103         xrefsAlignment = AlignmentUtils.makeCdsAlignment(
 104                 xrefsAlignment.getSequencesArray(), dataset, sel);
 105         xrefsAlignment.alignAs(alignment);
 106       }
 107
 108       /*
 109        * If we are opening a splitframe, make a copy of this alignment (sharing the same dataset
 110        * sequences). If we are DNA, drop introns and update mappings
 111        */
 112       AlignmentI copyAlignment = null;
 113
 114       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
 115       {
 116         boolean copyAlignmentIsAligned = false;
 117         if (dna)
 118         {
 119           copyAlignment = AlignmentUtils.makeCdsAlignment(sel, dataset,
 120                   xrefsAlignment.getSequencesArray());
 121           if (copyAlignment.getHeight() == 0)
 122           {
 123             JvOptionPane.showMessageDialog(alignFrame,
 124                     MessageManager.getString("label.cant_map_cds"),
 125                     MessageManager.getString("label.operation_failed"),
 126                     JvOptionPane.OK_OPTION);
 127             System.err.println("Failed to make CDS alignment");
 128           }
 129
 130           /*
 131            * pending getting Embl transcripts to 'align',
 132            * we are only doing this for Ensembl
 133            */
 134           // TODO proper criteria for 'can align as cdna'
 135           if (DBRefSource.ENSEMBL.equalsIgnoreCase(source)
 136                   || AlignmentUtils.looksLikeEnsembl(alignment))
 137           {
 138             copyAlignment.alignAs(alignment);
 139             copyAlignmentIsAligned = true;
 140           }
 141         }
 142         else
 143         {
 144           copyAlignment = AlignmentUtils.makeCopyAlignment(sel,
 145                   xrefs.getSequencesArray(), dataset);
 146         }
 147         copyAlignment
 148                 .setGapCharacter(alignFrame.viewport.getGapCharacter());
 149
 150         StructureSelectionManager ssm = StructureSelectionManager
 151                 .getStructureSelectionManager(Desktop.instance);
 152
 153         /*
 154          * register any new mappings for sequence mouseover etc
 155          * (will not duplicate any previously registered mappings)
 156          */
 157         ssm.registerMappings(dataset.getCodonFrames());
 158
 159         if (copyAlignment.getHeight() <= 0)
 160         {
 161           System.err.println(
 162                   "No Sequences generated for xRef type " + source);
 163           return;
 164         }
 165         /*
 166          * align protein to dna
 167          */
 168         if (dna && copyAlignmentIsAligned)
 169         {
 170           xrefsAlignment.alignAs(copyAlignment);
 171         }
 172         else
 173         {
 174           /*
 175            * align cdna to protein - currently only if
 176            * fetching and aligning Ensembl transcripts!
 177            */
 178           // TODO: generalise for other sources of locus/transcript/cds data
 179           if (dna && DBRefSource.ENSEMBL.equalsIgnoreCase(source))
 180           {
 181             copyAlignment.alignAs(xrefsAlignment);
 182           }
 183         }
 184       }
 185       /*
 186        * build AlignFrame(s) according to available alignment data
 187        */
 188       AlignFrame newFrame = new AlignFrame(xrefsAlignment,
 189               AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
 190       if (Cache.getDefault("HIDE_INTRONS", true))
 191       {
 192         newFrame.hideFeatureColumns(SequenceOntologyI.EXON, false);
 193       }
 194       String newtitle = String.format("%s %s %s",
 195               dna ? MessageManager.getString("label.proteins")
 196                       : MessageManager.getString("label.nucleotides"),
 197               MessageManager.getString("label.for"), alignFrame.getTitle());
 198       newFrame.setTitle(newtitle);
 199
 200       if (copyAlignment == null)
 201       {
 202         /*
 203          * split frame display is turned off in preferences file
 204          */
 205         Desktop.addInternalFrame(newFrame, newtitle,
 206                 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
 207         xrefViews.add(newFrame.alignPanel);
 208         return; // via finally clause
 209       }
 210       AlignFrame copyThis = new AlignFrame(copyAlignment,
 211               AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
 212       copyThis.setTitle(alignFrame.getTitle());
 213
 214       boolean showSequenceFeatures = alignFrame.getViewport()
 215               .isShowSequenceFeatures();
 216       newFrame.setShowSeqFeatures(showSequenceFeatures);
 217       copyThis.setShowSeqFeatures(showSequenceFeatures);
 218       FeatureRenderer myFeatureStyling = alignFrame.alignPanel
 219               .getSeqPanel().seqCanvas.getFeatureRenderer();
 220
 221       /*
 222        * copy feature rendering settings to split frame
 223        */
 224       newFrame.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
 225               .transferSettings(myFeatureStyling);
 226       copyThis.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
 227               .transferSettings(myFeatureStyling);
 228
 229       /*
 230        * apply 'database source' feature configuration
 231        * if any was found
 232        */
 233       // TODO is this the feature colouring for the original
 234       // alignment or the fetched xrefs? either could be Ensembl
 235       newFrame.getViewport().applyFeaturesStyle(featureColourScheme);
 236       copyThis.getViewport().applyFeaturesStyle(featureColourScheme);
 237
 238       SplitFrame sf = new SplitFrame(dna ? copyThis : newFrame,
 239               dna ? newFrame : copyThis);
 240       newFrame.setVisible(true);
 241       copyThis.setVisible(true);
 242       String linkedTitle = MessageManager
 243               .getString("label.linked_view_title");
 244       Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
 245       sf.adjustDivider();
 246
 247       // finally add the top, then bottom frame to the view list
 248       xrefViews.add(dna ? copyThis.alignPanel : newFrame.alignPanel);
 249       xrefViews.add(!dna ? copyThis.alignPanel : newFrame.alignPanel);
 250
 251     } catch (OutOfMemoryError e)
 252     {
 253       new OOMWarning("whilst fetching crossreferences", e);
 254     } catch (Throwable e)
 255     {
 256       Cache.log.error("Error when finding crossreferences", e);
 257     } finally
 258     {
 259       alignFrame.setProgressBar(MessageManager.formatMessage(
 260               "status.finished_searching_for_sequences_from", new Object[]
 261               { source }), sttime);
 262     }
 263   }
 264
 265   /**
 266    * Makes an alignment containing the given sequences, and adds them to the
 267    * given dataset, which is also set as the dataset for the new alignment
 268    *
 269    * TODO: refactor to DatasetI method
 270    *
 271    * @param dataset
 272    * @param seqs
 273    * @return
 274    */
 275   protected AlignmentI makeCrossReferencesAlignment(AlignmentI dataset,
 276           AlignmentI seqs)
 277   {
 278     SequenceI[] sprods = new SequenceI[seqs.getHeight()];
 279     for (int s = 0; s < sprods.length; s++)
 280     {
 281       sprods[s] = (seqs.getSequenceAt(s)).deriveSequence();
 282       if (dataset.getSequences() == null || !dataset.getSequences()
 283               .contains(sprods[s].getDatasetSequence()))
 284       {
 285         dataset.addSequence(sprods[s].getDatasetSequence());
 286       }
 287       sprods[s].updatePDBIds();
 288     }
 289     Alignment al = new Alignment(sprods);
 290     al.setDataset(dataset);
 291     return al;
 292   }
 293
 294   public CrossRefAction(AlignFrame alignFrame, SequenceI[] sel,
 295           boolean _odna, String source)
 296   {
 297     this.alignFrame = alignFrame;
 298     this.sel = sel;
 299     this._odna = _odna;
 300     this.source = source;
 301   }
 302
 303   public static CrossRefAction showProductsFor(final SequenceI[] sel,
 304           final boolean _odna, final String source,
 305           final AlignFrame alignFrame)
 306   {
 307     return new CrossRefAction(alignFrame, sel, _odna, source);
 308   }
 309
 310 }