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(
  71             MessageManager.formatMessage(
  72                     "status.searching_for_sequences_from",
  73                     new Object[] { source }), sttime);
  74     try
  75     {
  76       AlignmentI alignment = alignFrame.getViewport().getAlignment();
  77       AlignmentI dataset = alignment.getDataset() == null ? alignment
  78               : alignment.getDataset();
  79       boolean dna = alignment.isNucleotide();
  80       if (_odna != dna)
  81       {
  82         System.err
  83                 .println("Conflict: showProducts for alignment originally "
  84                         + "thought to be " + (_odna ? "DNA" : "Protein")
  85                         + " now searching for " + (dna ? "DNA" : "Protein")
  86                         + " Context.");
  87       }
  88       AlignmentI xrefs = new CrossRef(sel, dataset).findXrefSequences(
  89               source, dna);
  90       if (xrefs == null)
  91       {
  92         return;
  93       }
  94       /*
  95        * get display scheme (if any) to apply to features
  96        */
  97       FeatureSettingsModelI featureColourScheme = new SequenceFetcher()
  98               .getFeatureColourScheme(source);
  99
 100       AlignmentI xrefsAlignment = makeCrossReferencesAlignment(dataset,
 101               xrefs);
 102       if (!dna)
 103       {
 104         xrefsAlignment = AlignmentUtils.makeCdsAlignment(
 105                 xrefsAlignment.getSequencesArray(), dataset, sel);
 106         xrefsAlignment.alignAs(alignment);
 107       }
 108
 109       /*
 110        * If we are opening a splitframe, make a copy of this alignment (sharing the same dataset
 111        * sequences). If we are DNA, drop introns and update mappings
 112        */
 113       AlignmentI copyAlignment = null;
 114
 115       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
 116       {
 117         boolean copyAlignmentIsAligned = false;
 118         if (dna)
 119         {
 120           copyAlignment = AlignmentUtils.makeCdsAlignment(sel, dataset,
 121                   xrefsAlignment.getSequencesArray());
 122           if (copyAlignment.getHeight() == 0)
 123           {
 124             JvOptionPane.showMessageDialog(alignFrame,
 125                     MessageManager.getString("label.cant_map_cds"),
 126                     MessageManager.getString("label.operation_failed"),
 127                     JvOptionPane.OK_OPTION);
 128             System.err.println("Failed to make CDS alignment");
 129           }
 130
 131           /*
 132            * pending getting Embl transcripts to 'align',
 133            * we are only doing this for Ensembl
 134            */
 135           // TODO proper criteria for 'can align as cdna'
 136           if (DBRefSource.ENSEMBL.equalsIgnoreCase(source)
 137                   || AlignmentUtils.looksLikeEnsembl(alignment))
 138           {
 139             copyAlignment.alignAs(alignment);
 140             copyAlignmentIsAligned = true;
 141           }
 142         }
 143         else
 144         {
 145           copyAlignment = AlignmentUtils.makeCopyAlignment(sel,
 146                   xrefs.getSequencesArray(), dataset);
 147         }
 148         copyAlignment
 149                 .setGapCharacter(alignFrame.viewport.getGapCharacter());
 150
 151         StructureSelectionManager ssm = StructureSelectionManager
 152                 .getStructureSelectionManager(Desktop.instance);
 153
 154         /*
 155          * register any new mappings for sequence mouseover etc
 156          * (will not duplicate any previously registered mappings)
 157          */
 158         ssm.registerMappings(dataset.getCodonFrames());
 159
 160         if (copyAlignment.getHeight() <= 0)
 161         {
 162           System.err.println("No Sequences generated for xRef type "
 163                   + source);
 164           return;
 165         }
 166         /*
 167          * align protein to dna
 168          */
 169         if (dna && copyAlignmentIsAligned)
 170         {
 171           xrefsAlignment.alignAs(copyAlignment);
 172         }
 173         else
 174         {
 175           /*
 176            * align cdna to protein - currently only if
 177            * fetching and aligning Ensembl transcripts!
 178            */
 179           // TODO: generalise for other sources of locus/transcript/cds data
 180           if (dna && DBRefSource.ENSEMBL.equalsIgnoreCase(source))
 181           {
 182             copyAlignment.alignAs(xrefsAlignment);
 183           }
 184         }
 185       }
 186       /*
 187        * build AlignFrame(s) according to available alignment data
 188        */
 189       AlignFrame newFrame = new AlignFrame(xrefsAlignment,
 190               AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
 191       if (Cache.getDefault("HIDE_INTRONS", true))
 192       {
 193         newFrame.hideFeatureColumns(SequenceOntologyI.EXON, false);
 194       }
 195       String newtitle = String.format("%s %s %s",
 196               dna ? MessageManager.getString("label.proteins")
 197                       : MessageManager.getString("label.nucleotides"),
 198               MessageManager.getString("label.for"), alignFrame.getTitle());
 199       newFrame.setTitle(newtitle);
 200
 201       if (copyAlignment == null)
 202       {
 203         /*
 204          * split frame display is turned off in preferences file
 205          */
 206         Desktop.addInternalFrame(newFrame, newtitle,
 207                 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
 208         xrefViews.add(newFrame.alignPanel);
 209         return; // via finally clause
 210       }
 211       AlignFrame copyThis = new AlignFrame(copyAlignment,
 212               AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
 213       copyThis.setTitle(alignFrame.getTitle());
 214
 215       boolean showSequenceFeatures = alignFrame.getViewport()
 216               .isShowSequenceFeatures();
 217       newFrame.setShowSeqFeatures(showSequenceFeatures);
 218       copyThis.setShowSeqFeatures(showSequenceFeatures);
 219       FeatureRenderer myFeatureStyling = alignFrame.alignPanel
 220               .getSeqPanel().seqCanvas.getFeatureRenderer();
 221
 222       /*
 223        * copy feature rendering settings to split frame
 224        */
 225       newFrame.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
 226               .transferSettings(myFeatureStyling);
 227       copyThis.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
 228               .transferSettings(myFeatureStyling);
 229
 230       /*
 231        * apply 'database source' feature configuration
 232        * if any was found
 233        */
 234       // TODO is this the feature colouring for the original
 235       // alignment or the fetched xrefs? either could be Ensembl
 236       newFrame.getViewport().applyFeaturesStyle(featureColourScheme);
 237       copyThis.getViewport().applyFeaturesStyle(featureColourScheme);
 238
 239       SplitFrame sf = new SplitFrame(dna ? copyThis : newFrame,
 240               dna ? newFrame : copyThis);
 241       newFrame.setVisible(true);
 242       copyThis.setVisible(true);
 243       String linkedTitle = MessageManager
 244               .getString("label.linked_view_title");
 245       Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
 246       sf.adjustDivider();
 247
 248       // finally add the top, then bottom frame to the view list
 249       xrefViews.add(dna ? copyThis.alignPanel : newFrame.alignPanel);
 250       xrefViews.add(!dna ? copyThis.alignPanel : newFrame.alignPanel);
 251
 252     } catch (OutOfMemoryError e)
 253     {
 254       new OOMWarning("whilst fetching crossreferences", e);
 255     } catch (Throwable e)
 256     {
 257       Cache.log.error("Error when finding crossreferences", e);
 258     } finally
 259     {
 260       alignFrame.setProgressBar(MessageManager.formatMessage(
 261               "status.finished_searching_for_sequences_from",
 262               new Object[] { source }), sttime);
 263     }
 264   }
 265
 266   /**
 267    * Makes an alignment containing the given sequences, and adds them to the
 268    * given dataset, which is also set as the dataset for the new alignment
 269    *
 270    * TODO: refactor to DatasetI method
 271    *
 272    * @param dataset
 273    * @param seqs
 274    * @return
 275    */
 276   protected AlignmentI makeCrossReferencesAlignment(AlignmentI dataset,
 277           AlignmentI seqs)
 278   {
 279     SequenceI[] sprods = new SequenceI[seqs.getHeight()];
 280     for (int s = 0; s < sprods.length; s++)
 281     {
 282       sprods[s] = (seqs.getSequenceAt(s)).deriveSequence();
 283       if (dataset.getSequences() == null
 284               || !dataset.getSequences().contains(
 285                       sprods[s].getDatasetSequence()))
 286       {
 287         dataset.addSequence(sprods[s].getDatasetSequence());
 288       }
 289       sprods[s].updatePDBIds();
 290     }
 291     Alignment al = new Alignment(sprods);
 292     al.setDataset(dataset);
 293     return al;
 294   }
 295
 296   public CrossRefAction(AlignFrame alignFrame, SequenceI[] sel,
 297           boolean _odna, String source)
 298   {
 299     this.alignFrame = alignFrame;
 300     this.sel = sel;
 301     this._odna = _odna;
 302     this.source = source;
 303   }
 304
 305   public static CrossRefAction showProductsFor(final SequenceI[] sel,
 306           final boolean _odna, final String source,
 307           final AlignFrame alignFrame)
 308   {
 309     return new CrossRefAction(alignFrame, sel, _odna, source);
 310   }
 311
 312 }