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