X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=5ac946ad23d4dcbb69c2c01bc4e42542095a57e8;hb=bbfdb203ce3a889600caa52478478b75ab03809f;hp=0cbbdb496ab70751cf89b20a66ccd1252fa48813;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java old mode 100755 new mode 100644 index 0cbbdb4..5ac946a --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) - * 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.*; @@ -48,14 +49,15 @@ import jalview.datamodel.*; import jalview.schemes.*; import jalview.structure.SelectionSource; import jalview.structure.StructureSelectionManager; +import jalview.structure.VamsasSource; /** * DOCUMENT ME! * * @author $author$ - * @version $Revision$ + * @version $Revision: 1.141 $ */ -public class AlignViewport implements SelectionSource +public class AlignViewport implements SelectionSource, VamsasSource { private static final int RIGHT_JUSTIFY = 1; @@ -138,8 +140,12 @@ public class AlignViewport implements SelectionSource /** DOCUMENT ME!! */ public Hashtable[] hconsensus; + public Hashtable[] hStrucConsensus; + AlignmentAnnotation consensus; + AlignmentAnnotation strucConsensus; + AlignmentAnnotation conservation; AlignmentAnnotation quality; @@ -150,6 +156,8 @@ public class AlignViewport implements SelectionSource boolean autoCalculateConsensus = true; + boolean autoCalculateStrucConsensus = true; + /** DOCUMENT ME!! */ public int ConsPercGaps = 25; // JBPNote : This should be a scalable property! @@ -396,6 +404,7 @@ public class AlignViewport implements SelectionSource showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true); showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false); + normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO", false); showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false); // TODO: add menu option action that nulls or creates consensus object // depending on if the user wants to see the annotation or not in a @@ -405,10 +414,24 @@ public class AlignViewport implements SelectionSource 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) @@ -433,6 +456,8 @@ public class AlignViewport implements SelectionSource showUnconserved = jalview.bin.Cache.getDefault("SHOW_UNCONSERVED", false); sortByTree = jalview.bin.Cache.getDefault("SORT_BY_TREE", false); + followSelection = jalview.bin.Cache.getDefault("FOLLOW_SELECTIONS", + true); } /** @@ -455,14 +480,20 @@ public class AlignViewport implements SelectionSource 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; /** @@ -476,11 +507,6 @@ public class AlignViewport implements SelectionSource private boolean shownpfeats; /** - * consensus annotation includes all percentage for all symbols in column - */ - private boolean includeAllConsensusSymbols = true; - - /** * trigger update of conservation annotation */ public void updateConservation(final AlignmentPanel ap) @@ -542,12 +568,14 @@ public class AlignViewport implements SelectionSource try { - int aWidth = (alignment != null) ? alignment.getWidth() : 0; // null + int aWidth = (alignment != null) ? alignment.getWidth() : -1; // null // pointer // possibility // here. - if (aWidth < 0) + if (aWidth <= 0) { + updatingConsensus = false; + UPDATING_CONSENSUS = false; return; } @@ -556,11 +584,8 @@ public class AlignViewport implements SelectionSource hconsensus = new Hashtable[aWidth]; AAFrequency.calculate(alignment.getSequencesArray(), 0, alignment - .getWidth(), hconsensus, includeAllConsensusSymbols); - AAFrequency.completeConsensus(consensus, hconsensus, 0, aWidth, - ignoreGapsInConsensusCalculation, - includeAllConsensusSymbols); - + .getWidth(), hconsensus, true); + updateAnnotation(true); if (globalColourScheme != null) { globalColourScheme.setConsensus(hconsensus); @@ -582,8 +607,155 @@ public class AlignViewport implements SelectionSource 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 + || (!updatingConsensus && consensus != null && hconsensus != null)) + { + AAFrequency.completeConsensus(consensus, hconsensus, 0, + hconsensus.length, ignoreGapsInConsensusCalculation, + showSequenceLogo); + } + } + } + + // --------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. @@ -623,9 +795,9 @@ public class AlignViewport implements SelectionSource } /** - * DOCUMENT ME! * - * @return DOCUMENT ME! + * + * @return null or the currently selected sequence region */ public SequenceGroup getSelectionGroup() { @@ -633,10 +805,11 @@ public class AlignViewport implements SelectionSource } /** - * DOCUMENT ME! + * Set the selection group for this window. * * @param sg - * DOCUMENT ME! + * - group holding references to sequences in this alignment view + * */ public void setSelectionGroup(SequenceGroup sg) { @@ -644,9 +817,9 @@ public class AlignViewport implements SelectionSource } /** - * DOCUMENT ME! + * GUI state * - * @return DOCUMENT ME! + * @return true if conservation based shading is enabled */ public boolean getConservationSelected() { @@ -654,10 +827,10 @@ public class AlignViewport implements SelectionSource } /** - * DOCUMENT ME! + * GUI state * * @param b - * DOCUMENT ME! + * enable conservation based shading */ public void setConservationSelected(boolean b) { @@ -665,9 +838,9 @@ public class AlignViewport implements SelectionSource } /** - * DOCUMENT ME! + * GUI state * - * @return DOCUMENT ME! + * @return true if percent identity threshold is applied to shading */ public boolean getAbovePIDThreshold() { @@ -675,10 +848,11 @@ public class AlignViewport implements SelectionSource } /** - * DOCUMENT ME! + * GUI state + * * * @param b - * DOCUMENT ME! + * indicate if percent identity threshold is applied to shading */ public void setAbovePIDThreshold(boolean b) { @@ -923,14 +1097,14 @@ public class AlignViewport implements SelectionSource { 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()); } } @@ -1546,90 +1720,23 @@ public class AlignViewport implements SelectionSource public jalview.datamodel.CigarArray getViewAsCigars( boolean selectedRegionOnly) { - CigarArray selection = null; - SequenceI[] seqs = null; - int i, iSize; - int start = 0, end = 0; - if (selectedRegionOnly && selectionGroup != null) - { - iSize = selectionGroup.getSize(); - seqs = selectionGroup.getSequencesInOrder(alignment); - start = selectionGroup.getStartRes(); - end = selectionGroup.getEndRes(); // inclusive for start and end in - // SeqCigar constructor - } - else - { - iSize = alignment.getHeight(); - seqs = alignment.getSequencesArray(); - end = alignment.getWidth() - 1; - } - SeqCigar[] selseqs = new SeqCigar[iSize]; - for (i = 0; i < iSize; i++) - { - selseqs[i] = new SeqCigar(seqs[i], start, end); - } - selection = new CigarArray(selseqs); - // now construct the CigarArray operations - if (hasHiddenColumns) - { - Vector regions = colSel.getHiddenColumns(); - int[] region; - int hideStart, hideEnd; - int last = start; - for (int j = 0; last < end & j < regions.size(); j++) - { - region = (int[]) regions.elementAt(j); - hideStart = region[0]; - hideEnd = region[1]; - // edit hidden regions to selection range - if (hideStart < last) - { - if (hideEnd > last) - { - hideStart = last; - } - else - { - continue; - } - } - - if (hideStart > end) - { - break; - } - - if (hideEnd > end) - { - hideEnd = end; - } + return new jalview.datamodel.CigarArray(alignment, + (hasHiddenColumns ? colSel : null), + (selectedRegionOnly ? selectionGroup : null)); + } - if (hideStart > hideEnd) - { - break; - } - /** - * form operations... - */ - if (last < hideStart) - { - selection.addOperation(CigarArray.M, hideStart - last); - } - selection.addOperation(CigarArray.D, 1 + hideEnd - hideStart); - last = hideEnd + 1; - } - // Final match if necessary. - if (last < end) - { - selection.addOperation(CigarArray.M, end - last + 1); - } - } - else - { - selection.addOperation(CigarArray.M, end - start + 1); - } - return selection; + /** + * return a compact representation of the current alignment selection to pass + * to an analysis function + * + * @param selectedOnly + * boolean true to just return the selected view + * @return AlignmentView + */ + public jalview.datamodel.AlignmentView getAlignmentView( + boolean selectedOnly) + { + return getAlignmentView(selectedOnly, false); } /** @@ -1638,23 +1745,17 @@ public class AlignViewport implements SelectionSource * * @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) * @return AlignmentView */ - jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly) + public jalview.datamodel.AlignmentView getAlignmentView( + boolean selectedOnly, boolean markGroups) { - // JBPNote: - // this is here because the AlignmentView constructor modifies the - // CigarArray - // object. Refactoring of Cigar and alignment view representation should - // be done to remove redundancy. - CigarArray aligview = getViewAsCigars(selectedOnly); - if (aligview != null) - { - return new AlignmentView(aligview, - (selectedOnly && selectionGroup != null) ? selectionGroup - .getStartRes() : 0); - } - return null; + return new AlignmentView(alignment, colSel, selectionGroup, + hasHiddenColumns, selectedOnly, markGroups); } /** @@ -1794,6 +1895,10 @@ public class AlignViewport implements SelectionSource { updateConsensus(ap); } + if (autoCalculateStrucConsensus) + { + updateStrucConsensus(ap); + } // Reset endRes of groups if beyond alignment width int alWidth = alignment.getWidth(); @@ -2078,31 +2183,44 @@ public class AlignViewport implements SelectionSource * 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; @@ -2111,7 +2229,7 @@ public class AlignViewport implements SelectionSource public void sendSelection() { jalview.structure.StructureSelectionManager - .getStructureSelectionManager().sendSelection( + .getStructureSelectionManager(Desktop.instance).sendSelection( new SequenceGroup(getSelectionGroup()), new ColumnSelection(getColumnSelection()), this); } @@ -2185,7 +2303,10 @@ public class AlignViewport implements SelectionSource * should consensus profile be rendered by default */ public boolean showSequenceLogo = false; - + /** + * should consensus profile be rendered normalised to row height + */ + public boolean normaliseSequenceLogo = false; /** * should consensus histograms be rendered by default */ @@ -2205,6 +2326,20 @@ public class AlignViewport implements SelectionSource */ public void setShowSequenceLogo(boolean showSequenceLogo) { + if (showSequenceLogo != this.showSequenceLogo) + { + // TODO: decouple settings setting from calculation when refactoring + // annotation update method from alignframe to viewport + this.showSequenceLogo = showSequenceLogo; + if (consensusThread != null) + { + consensusThread.updateAnnotation(); + } + if (strucConsensusThread != null) + { + strucConsensusThread.updateAnnotation(); + } + } this.showSequenceLogo = showSequenceLogo; } @@ -2252,24 +2387,6 @@ public class AlignViewport implements SelectionSource } /** - * @return the includeAllConsensusSymbols - */ - public boolean isIncludeAllConsensusSymbols() - { - return includeAllConsensusSymbols; - } - - /** - * @param includeAllConsensusSymbols - * the includeAllConsensusSymbols to set - */ - public void setIncludeAllConsensusSymbols( - boolean includeAllConsensusSymbols) - { - this.includeAllConsensusSymbols = includeAllConsensusSymbols; - } - - /** * * @return flag to indicate if the consensus histogram should be rendered by * default @@ -2311,4 +2428,57 @@ public class AlignViewport implements SelectionSource } } } + + 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()][]); + } + + + public boolean isNormaliseSequenceLogo() + { + return normaliseSequenceLogo; + } + + public void setNormaliseSequenceLogo(boolean state) + { + normaliseSequenceLogo = state; + } }