X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=f5bc6e4cf3014e61522070c5bffd4270d833be39;hb=7aa643222eefde760ffe621bc1e04ca50713f66e;hp=ff21931ca327e94230cee87c8d71b2637e25ee99;hpb=df5ad7ed6689ae04034c3ade2c9d725de7619b68;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java old mode 100755 new mode 100644 index ff21931..f5bc6e4 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle * * This file is part of Jalview. * @@ -40,6 +40,7 @@ import java.util.*; import java.awt.*; import jalview.analysis.*; +import jalview.api.StructureSelectionManagerProvider; import jalview.bin.*; @@ -54,7 +55,7 @@ import jalview.structure.VamsasSource; * DOCUMENT ME! * * @author $author$ - * @version $Revision$ + * @version $Revision: 1.141 $ */ public class AlignViewport implements SelectionSource, VamsasSource { @@ -139,8 +140,12 @@ public class AlignViewport implements SelectionSource, VamsasSource /** DOCUMENT ME!! */ public Hashtable[] hconsensus; + public Hashtable[] hStrucConsensus; + AlignmentAnnotation consensus; + AlignmentAnnotation strucConsensus; + AlignmentAnnotation conservation; AlignmentAnnotation quality; @@ -151,6 +156,8 @@ public class AlignViewport implements SelectionSource, VamsasSource boolean autoCalculateConsensus = true; + boolean autoCalculateStrucConsensus = true; + /** DOCUMENT ME!! */ public int ConsPercGaps = 25; // JBPNote : This should be a scalable property! @@ -406,10 +413,24 @@ public class AlignViewport implements SelectionSource, VamsasSource consensus.hasText = true; consensus.autoCalculated = true; + if (alignment.isNucleotide() && alignment.hasRNAStructure()) + { + strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID", + new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); + strucConsensus.hasText = true; + strucConsensus.autoCalculated = true; + } + if (Cache.getDefault("SHOW_IDENTITY", true)) { alignment.addAnnotation(consensus); + // TODO: Make own if for structure + if (alignment.isNucleotide() && alignment.hasRNAStructure()) + { + alignment.addAnnotation(strucConsensus); + } } + } if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null) @@ -458,14 +479,20 @@ public class AlignViewport implements SelectionSource, VamsasSource ConsensusThread consensusThread; + StrucConsensusThread strucConsensusThread; + boolean consUpdateNeeded = false; static boolean UPDATING_CONSENSUS = false; + static boolean UPDATING_STRUC_CONSENSUS = false; + static boolean UPDATING_CONSERVATION = false; boolean updatingConsensus = false; + boolean updatingStrucConsensus = false; + boolean updatingConservation = false; /** @@ -555,10 +582,9 @@ public class AlignViewport implements SelectionSource, VamsasSource consensus.annotations = new Annotation[aWidth]; hconsensus = new Hashtable[aWidth]; - AAFrequency.calculate(alignment.getSequencesArray(), 0, - alignment.getWidth(), hconsensus, true); + AAFrequency.calculate(alignment.getSequencesArray(), 0, alignment + .getWidth(), hconsensus, true); updateAnnotation(true); - if (globalColourScheme != null) { globalColourScheme.setConsensus(hconsensus); @@ -604,6 +630,131 @@ public class AlignViewport implements SelectionSource, VamsasSource } } + // --------START Structure Conservation + public void updateStrucConsensus(final AlignmentPanel ap) + { + // see note in mantis : issue number 8585 + if (strucConsensus == null || !autoCalculateStrucConsensus) + { + return; + } + strucConsensusThread = new StrucConsensusThread(ap); + strucConsensusThread.start(); + } + + class StrucConsensusThread extends Thread + { + AlignmentPanel ap; + + public StrucConsensusThread(AlignmentPanel ap) + { + this.ap = ap; + } + + public void run() + { + updatingStrucConsensus = true; + while (UPDATING_STRUC_CONSENSUS) + { + try + { + if (ap != null) + { + ap.paintAlignment(false); + } + + Thread.sleep(200); + } catch (Exception ex) + { + ex.printStackTrace(); + } + } + + UPDATING_STRUC_CONSENSUS = true; + + try + { + int aWidth = (alignment != null) ? alignment.getWidth() : -1; // null + // pointer + // possibility + // here. + if (aWidth <= 0) + { + updatingStrucConsensus = false; + UPDATING_STRUC_CONSENSUS = false; + return; + } + + strucConsensus.annotations = null; + strucConsensus.annotations = new Annotation[aWidth]; + + hStrucConsensus = new Hashtable[aWidth]; + + AlignmentAnnotation[] aa = ap.av.getAlignment() + .getAlignmentAnnotation(); + AlignmentAnnotation rnaStruc = null; + for (int i = 0; i < aa.length; i++) + { + if (aa[i].getRNAStruc() != null) + { + rnaStruc = aa[i]; + break; + } + } + + AlignmentAnnotation rna = ap.av.getAlignment() + .getAlignmentAnnotation()[0]; + StructureFrequency.calculate(alignment.getSequencesArray(), 0, + alignment.getWidth(), hStrucConsensus, true, rnaStruc); + // TODO AlignmentAnnotation rnaStruc!!! + updateAnnotation(true); + if (globalColourScheme != null) + { + globalColourScheme.setConsensus(hStrucConsensus); + } + + } catch (OutOfMemoryError error) + { + alignment.deleteAnnotation(strucConsensus); + + strucConsensus = null; + hStrucConsensus = null; + new OOMWarning("calculating structure consensus", error); + } + UPDATING_STRUC_CONSENSUS = false; + updatingStrucConsensus = false; + + if (ap != null) + { + ap.paintAlignment(true); + } + } + + /** + * update the consensus annotation from the sequence profile data using + * current visualization settings. + */ + public void updateAnnotation() + { + updateAnnotation(false); + } + + protected void updateAnnotation(boolean immediate) + { + // TODO: make calls thread-safe, so if another thread calls this method, + // it will either return or wait until one calculation is finished. + if (immediate + || (!updatingStrucConsensus && strucConsensus != null && hStrucConsensus != null)) + { + StructureFrequency.completeConsensus(strucConsensus, + hStrucConsensus, 0, hStrucConsensus.length, false, + showSequenceLogo); + } + } + } + + // --------END Structure Conservation + /** * get the consensus sequence as displayed under the PID consensus annotation * row. @@ -655,8 +806,9 @@ public class AlignViewport implements SelectionSource, VamsasSource /** * Set the selection group for this window. * - * @param sg - group holding references to sequences in this alignment view - * + * @param sg + * - group holding references to sequences in this alignment view + * */ public void setSelectionGroup(SequenceGroup sg) { @@ -665,6 +817,7 @@ public class AlignViewport implements SelectionSource, VamsasSource /** * GUI state + * * @return true if conservation based shading is enabled */ public boolean getConservationSelected() @@ -674,6 +827,7 @@ public class AlignViewport implements SelectionSource, VamsasSource /** * GUI state + * * @param b * enable conservation based shading */ @@ -684,6 +838,7 @@ public class AlignViewport implements SelectionSource, VamsasSource /** * GUI state + * * @return true if percent identity threshold is applied to shading */ public boolean getAbovePIDThreshold() @@ -695,7 +850,8 @@ public class AlignViewport implements SelectionSource, VamsasSource * GUI state * * - * @param b indicate if percent identity threshold is applied to shading + * @param b + * indicate if percent identity threshold is applied to shading */ public void setAbovePIDThreshold(boolean b) { @@ -940,14 +1096,14 @@ public class AlignViewport implements SelectionSource, VamsasSource { if (alignment != null && alignment.getCodonFrames() != null) { - StructureSelectionManager.getStructureSelectionManager() - .removeMappings(alignment.getCodonFrames()); + StructureSelectionManager.getStructureSelectionManager( + Desktop.instance).removeMappings(alignment.getCodonFrames()); } this.alignment = align; if (alignment.getCodonFrames() != null) { - StructureSelectionManager.getStructureSelectionManager().addMappings( - alignment.getCodonFrames()); + StructureSelectionManager.getStructureSelectionManager( + Desktop.instance).addMappings(alignment.getCodonFrames()); } } @@ -1563,7 +1719,9 @@ public class AlignViewport implements SelectionSource, VamsasSource public jalview.datamodel.CigarArray getViewAsCigars( boolean selectedRegionOnly) { - return new jalview.datamodel.CigarArray(alignment, (hasHiddenColumns ? colSel : null), (selectedRegionOnly ? selectionGroup : null)); + return new jalview.datamodel.CigarArray(alignment, + (hasHiddenColumns ? colSel : null), + (selectedRegionOnly ? selectionGroup : null)); } /** @@ -1574,11 +1732,12 @@ public class AlignViewport implements SelectionSource, VamsasSource * boolean true to just return the selected view * @return AlignmentView */ - public jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly) + public jalview.datamodel.AlignmentView getAlignmentView( + boolean selectedOnly) { return getAlignmentView(selectedOnly, false); } - + /** * return a compact representation of the current alignment selection to pass * to an analysis function @@ -1586,12 +1745,16 @@ public class AlignViewport implements SelectionSource, VamsasSource * @param selectedOnly * boolean true to just return the selected view * @param markGroups - * boolean true to annotate the alignment view with groups on the alignment (and intersecting with selected region if selectedOnly is true) + * boolean true to annotate the alignment view with groups on the + * alignment (and intersecting with selected region if selectedOnly + * is true) * @return AlignmentView */ - public jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly, boolean markGroups) + public jalview.datamodel.AlignmentView getAlignmentView( + boolean selectedOnly, boolean markGroups) { - return new AlignmentView(alignment, colSel, selectionGroup, hasHiddenColumns, selectedOnly, markGroups); + return new AlignmentView(alignment, colSel, selectionGroup, + hasHiddenColumns, selectedOnly, markGroups); } /** @@ -1731,6 +1894,10 @@ public class AlignViewport implements SelectionSource, VamsasSource { updateConsensus(ap); } + if (autoCalculateStrucConsensus) + { + updateStrucConsensus(ap); + } // Reset endRes of groups if beyond alignment width int alWidth = alignment.getWidth(); @@ -1773,8 +1940,8 @@ public class AlignViewport implements SelectionSource, VamsasSource { Alignment al = (Alignment) alignment; Conservation c = new Conservation("All", - ResidueProperties.propHash, 3, al.getSequences(), 0, - al.getWidth() - 1); + ResidueProperties.propHash, 3, al.getSequences(), 0, al + .getWidth() - 1); c.calculate(); c.verdict(false, ConsPercGaps); @@ -1788,8 +1955,8 @@ public class AlignViewport implements SelectionSource, VamsasSource SequenceGroup sg = (SequenceGroup) alignment.getGroups().elementAt(s); if (sg.cs != null && sg.cs instanceof ClustalxColourScheme) { - ((ClustalxColourScheme) sg.cs).resetClustalX( - sg.getSequences(hiddenRepSequences), sg.getWidth()); + ((ClustalxColourScheme) sg.cs).resetClustalX(sg + .getSequences(hiddenRepSequences), sg.getWidth()); } sg.recalcConservation(); } @@ -2015,31 +2182,44 @@ public class AlignViewport implements SelectionSource, VamsasSource * checks current SelectionGroup against record of last hash value, and * updates record. * - * @return true if SelectionGroup changed since last call + * @param b + * update the record of last hash value + * + * @return true if SelectionGroup changed since last call (when b is true) */ - boolean isSelectionGroupChanged() + boolean isSelectionGroupChanged(boolean b) { - int hc = (selectionGroup == null) ? -1 : selectionGroup.hashCode(); - if (hc != sgrouphash) + int hc = (selectionGroup == null || selectionGroup.getSize() == 0) ? -1 + : selectionGroup.hashCode(); + if (hc != -1 && hc != sgrouphash) { - sgrouphash = hc; + if (b) + { + sgrouphash = hc; + } return true; } return false; } /** - * checks current colsel against record of last hash value, and updates - * record. + * checks current colsel against record of last hash value, and optionally + * updates record. * - * @return true if colsel changed since last call + * @param b + * update the record of last hash value + * @return true if colsel changed since last call (when b is true) */ - boolean isColSelChanged() + boolean isColSelChanged(boolean b) { - int hc = (colSel == null) ? -1 : colSel.hashCode(); - if (hc != colselhash) + int hc = (colSel == null || colSel.size() == 0) ? -1 : colSel + .hashCode(); + if (hc != -1 && hc != colselhash) { - colselhash = hc; + if (b) + { + colselhash = hc; + } return true; } return false; @@ -2048,7 +2228,7 @@ public class AlignViewport implements SelectionSource, VamsasSource public void sendSelection() { jalview.structure.StructureSelectionManager - .getStructureSelectionManager().sendSelection( + .getStructureSelectionManager(Desktop.instance).sendSelection( new SequenceGroup(getSelectionGroup()), new ColumnSelection(getColumnSelection()), this); } @@ -2151,6 +2331,10 @@ public class AlignViewport implements SelectionSource, VamsasSource { consensusThread.updateAnnotation(); } + if (strucConsensusThread != null) + { + strucConsensusThread.updateAnnotation(); + } } this.showSequenceLogo = showSequenceLogo; } @@ -2240,4 +2424,46 @@ public class AlignViewport implements SelectionSource, VamsasSource } } } + + public StructureSelectionManager getStructureSelectionManager() + { + return StructureSelectionManager + .getStructureSelectionManager(Desktop.instance); + } + + /** + * + * @param pdbEntries + * @return a series of SequenceI arrays, one for each PDBEntry, listing which + * sequence in the alignment holds a reference to it + */ + public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries) + { + ArrayList seqvectors = new ArrayList(); + for (PDBEntry pdb : pdbEntries) + { + ArrayList seqs = new ArrayList(); + for (int i = 0; i < alignment.getHeight(); i++) + { + Vector pdbs = alignment.getSequenceAt(i).getDatasetSequence() + .getPDBId(); + if (pdbs == null) + continue; + SequenceI sq; + for (int p = 0; p < pdbs.size(); p++) + { + PDBEntry p1 = (PDBEntry) pdbs.elementAt(p); + if (p1.getId().equals(pdb.getId())) + { + if (!seqs.contains(sq = alignment.getSequenceAt(i))) + seqs.add(sq); + + continue; + } + } + } + seqvectors.add(seqs.toArray(new SequenceI[seqs.size()])); + } + return seqvectors.toArray(new SequenceI[seqvectors.size()][]); + } }