X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=c168b7b8d527fd2cbb312bbba417b3e9ef70e85c;hb=d053a3c980cf4318b9a19a255f9fc870e74de989;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..c168b7b --- 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 +40,10 @@ import java.util.*; import java.awt.*; import jalview.analysis.*; +import jalview.api.AlignCalcManagerI; +import jalview.api.AlignViewportI; +import jalview.api.AlignmentViewPanel; +import jalview.api.OOMHandlerI; import jalview.bin.*; @@ -49,14 +53,19 @@ import jalview.schemes.*; import jalview.structure.SelectionSource; import jalview.structure.StructureSelectionManager; import jalview.structure.VamsasSource; +import jalview.viewmodel.AlignmentViewport; +import jalview.workers.AlignCalcManager; +import jalview.workers.ConsensusThread; +import jalview.workers.ConservationThread; +import jalview.workers.StrucConsensusThread; /** * DOCUMENT ME! * * @author $author$ - * @version $Revision$ + * @version $Revision: 1.141 $ */ -public class AlignViewport implements SelectionSource, VamsasSource +public class AlignViewport extends AlignmentViewport implements SelectionSource, VamsasSource, AlignViewportI { private static final int RIGHT_JUSTIFY = 1; @@ -86,14 +95,10 @@ public class AlignViewport implements SelectionSource, VamsasSource boolean colourAppliesToAllGroups = true; - ColourSchemeI globalColourScheme = null; - boolean conservationColourSelected = false; boolean abovePIDThreshold = false; - SequenceGroup selectionGroup; - int charHeight; int charWidth; @@ -106,10 +111,6 @@ public class AlignViewport implements SelectionSource, VamsasSource boolean seqNameItalics; - AlignmentI alignment; - - ColumnSelection colSel = new ColumnSelection(); - int threshold; int increment; @@ -122,10 +123,6 @@ public class AlignViewport implements SelectionSource, VamsasSource boolean scaleRightWrapped = true; - boolean hasHiddenColumns = false; - - boolean hasHiddenRows = false; - boolean showHiddenMarkers = true; boolean cursorMode = false; @@ -136,42 +133,15 @@ public class AlignViewport implements SelectionSource, VamsasSource */ Hashtable featuresDisplayed = null; - /** DOCUMENT ME!! */ - public Hashtable[] hconsensus; - - AlignmentAnnotation consensus; - - AlignmentAnnotation conservation; - - AlignmentAnnotation quality; - - AlignmentAnnotation[] groupConsensus; - - AlignmentAnnotation[] groupConservation; - - boolean autoCalculateConsensus = true; - - /** DOCUMENT ME!! */ - public int ConsPercGaps = 25; // JBPNote : This should be a scalable property! - - // JBPNote Prolly only need this in the applet version. - private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport( - this); - - boolean ignoreGapsInConsensusCalculation = false; boolean isDataset = false; boolean antiAlias = false; - boolean padGaps = false; - Rectangle explodedPosition; String viewName; - String sequenceSetID; - boolean gatherViewsHere = false; Stack historyList = new Stack(); @@ -188,10 +158,6 @@ public class AlignViewport implements SelectionSource, VamsasSource boolean rightAlignIds = false; - Hashtable hiddenRepSequences; - - boolean sortByTree; - /** * Creates a new AlignViewport object. * @@ -333,7 +299,7 @@ public class AlignViewport implements SelectionSource, VamsasSource centreColumnLabels = Cache.getDefault("CENTRE_COLUMN_LABELS", false); autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true); - padGaps = Cache.getDefault("PAD_GAPS", true); + setPadGaps(Cache.getDefault("PAD_GAPS", true)); shownpfeats = Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true); showdbrefs = Cache.getDefault("SHOW_DBREFS_TOOLTIP", true); @@ -366,7 +332,7 @@ public class AlignViewport implements SelectionSource, VamsasSource if (!alignment.isNucleotide()) { conservation = new AlignmentAnnotation("Conservation", - "Conservation of total alignment less than " + ConsPercGaps + "Conservation of total alignment less than " + getConsPercGaps() + "% gaps", new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH); conservation.hasText = true; @@ -397,6 +363,7 @@ public class AlignViewport implements SelectionSource, VamsasSource 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 @@ -406,10 +373,24 @@ 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) @@ -454,20 +435,6 @@ public class AlignViewport implements SelectionSource, VamsasSource return showSequenceFeatures; } - ConservationThread conservationThread; - - ConsensusThread consensusThread; - - boolean consUpdateNeeded = false; - - static boolean UPDATING_CONSENSUS = false; - - static boolean UPDATING_CONSERVATION = false; - - boolean updatingConsensus = false; - - boolean updatingConservation = false; - /** * centre columnar annotation labels in displayed alignment annotation TODO: * add to jalviewXML and annotation display settings @@ -478,131 +445,7 @@ public class AlignViewport implements SelectionSource, VamsasSource private boolean shownpfeats; - /** - * trigger update of conservation annotation - */ - public void updateConservation(final AlignmentPanel ap) - { - // see note in mantis : issue number 8585 - if (alignment.isNucleotide() || conservation == null - || !autoCalculateConsensus) - { - return; - } - - conservationThread = new ConservationThread(this, ap); - conservationThread.start(); - } - - /** - * trigger update of consensus annotation - */ - public void updateConsensus(final AlignmentPanel ap) - { - // see note in mantis : issue number 8585 - if (consensus == null || !autoCalculateConsensus) - { - return; - } - consensusThread = new ConsensusThread(ap); - consensusThread.start(); - } - - class ConsensusThread extends Thread - { - AlignmentPanel ap; - - public ConsensusThread(AlignmentPanel ap) - { - this.ap = ap; - } - - public void run() - { - updatingConsensus = true; - while (UPDATING_CONSENSUS) - { - try - { - if (ap != null) - { - ap.paintAlignment(false); - } - - Thread.sleep(200); - } catch (Exception ex) - { - ex.printStackTrace(); - } - } - - UPDATING_CONSENSUS = true; - - try - { - int aWidth = (alignment != null) ? alignment.getWidth() : -1; // null - // pointer - // possibility - // here. - if (aWidth <= 0) - { - updatingConsensus = false; - UPDATING_CONSENSUS = false; - return; - } - - consensus.annotations = null; - consensus.annotations = new Annotation[aWidth]; - - hconsensus = new Hashtable[aWidth]; - AAFrequency.calculate(alignment.getSequencesArray(), 0, - alignment.getWidth(), hconsensus, true); - updateAnnotation(true); - - if (globalColourScheme != null) - { - globalColourScheme.setConsensus(hconsensus); - } - - } catch (OutOfMemoryError error) - { - alignment.deleteAnnotation(consensus); - - consensus = null; - hconsensus = null; - new OOMWarning("calculating consensus", error); - } - UPDATING_CONSENSUS = false; - updatingConsensus = 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 - || (!updatingConsensus && consensus != null && hconsensus != null)) - { - AAFrequency.completeConsensus(consensus, hconsensus, 0, - hconsensus.length, ignoreGapsInConsensusCalculation, - showSequenceLogo); - } - } - } + // --------END Structure Conservation /** * get the consensus sequence as displayed under the PID consensus annotation @@ -642,29 +485,10 @@ public class AlignViewport implements SelectionSource, VamsasSource return sq; } - /** - * - * - * @return null or the currently selected sequence region - */ - public SequenceGroup getSelectionGroup() - { - return selectionGroup; - } - - /** - * Set the selection group for this window. - * - * @param sg - group holding references to sequences in this alignment view - * - */ - public void setSelectionGroup(SequenceGroup sg) - { - selectionGroup = sg; - } /** * GUI state + * * @return true if conservation based shading is enabled */ public boolean getConservationSelected() @@ -674,6 +498,7 @@ public class AlignViewport implements SelectionSource, VamsasSource /** * GUI state + * * @param b * enable conservation based shading */ @@ -684,6 +509,7 @@ public class AlignViewport implements SelectionSource, VamsasSource /** * GUI state + * * @return true if percent identity threshold is applied to shading */ public boolean getAbovePIDThreshold() @@ -695,7 +521,8 @@ 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) { @@ -735,27 +562,6 @@ public class AlignViewport implements SelectionSource, VamsasSource /** * DOCUMENT ME! * - * @param cs - * DOCUMENT ME! - */ - public void setGlobalColourScheme(ColourSchemeI cs) - { - globalColourScheme = cs; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public ColourSchemeI getGlobalColourScheme() - { - return globalColourScheme; - } - - /** - * DOCUMENT ME! - * * @param res * DOCUMENT ME! */ @@ -940,14 +746,14 @@ 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) + if (alignment!=null && alignment.getCodonFrames() != null) { - StructureSelectionManager.getStructureSelectionManager().addMappings( - alignment.getCodonFrames()); + StructureSelectionManager.getStructureSelectionManager( + Desktop.instance).addMappings(alignment.getCodonFrames()); } } @@ -1269,61 +1075,6 @@ public class AlignViewport implements SelectionSource, VamsasSource scaleRightWrapped = b; } - /** - * Property change listener for changes in alignment - * - * @param listener - * DOCUMENT ME! - */ - public void addPropertyChangeListener( - java.beans.PropertyChangeListener listener) - { - changeSupport.addPropertyChangeListener(listener); - } - - /** - * DOCUMENT ME! - * - * @param listener - * DOCUMENT ME! - */ - public void removePropertyChangeListener( - java.beans.PropertyChangeListener listener) - { - changeSupport.removePropertyChangeListener(listener); - } - - /** - * Property change listener for changes in alignment - * - * @param prop - * DOCUMENT ME! - * @param oldvalue - * DOCUMENT ME! - * @param newvalue - * DOCUMENT ME! - */ - public void firePropertyChange(String prop, Object oldvalue, - Object newvalue) - { - changeSupport.firePropertyChange(prop, oldvalue, newvalue); - } - - public void setIgnoreGapsConsensus(boolean b, AlignmentPanel ap) - { - ignoreGapsInConsensusCalculation = b; - updateConsensus(ap); - if (globalColourScheme != null) - { - globalColourScheme.setThreshold(globalColourScheme.getThreshold(), - ignoreGapsInConsensusCalculation); - } - } - - public boolean getIgnoreGapsConsensus() - { - return ignoreGapsInConsensusCalculation; - } public void setDataset(boolean b) { @@ -1335,352 +1086,7 @@ public class AlignViewport implements SelectionSource, VamsasSource return isDataset; } - public void hideSelectedColumns() - { - if (colSel.size() < 1) - { - return; - } - - colSel.hideSelectedColumns(); - setSelectionGroup(null); - - hasHiddenColumns = true; - } - - public void hideColumns(int start, int end) - { - if (start == end) - { - colSel.hideColumns(start); - } - else - { - colSel.hideColumns(start, end); - } - - hasHiddenColumns = true; - } - - public void hideRepSequences(SequenceI repSequence, SequenceGroup sg) - { - int sSize = sg.getSize(); - if (sSize < 2) - { - return; - } - - if (hiddenRepSequences == null) - { - hiddenRepSequences = new Hashtable(); - } - - hiddenRepSequences.put(repSequence, sg); - - // Hide all sequences except the repSequence - SequenceI[] seqs = new SequenceI[sSize - 1]; - int index = 0; - for (int i = 0; i < sSize; i++) - { - if (sg.getSequenceAt(i) != repSequence) - { - if (index == sSize - 1) - { - return; - } - - seqs[index++] = sg.getSequenceAt(i); - } - } - sg.setSeqrep(repSequence); - sg.setHidereps(true); - hideSequence(seqs); - - } - - public void hideAllSelectedSeqs() - { - if (selectionGroup == null || selectionGroup.getSize() < 1) - { - return; - } - - SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment); - - hideSequence(seqs); - - setSelectionGroup(null); - } - - public void hideSequence(SequenceI[] seq) - { - if (seq != null) - { - for (int i = 0; i < seq.length; i++) - { - alignment.getHiddenSequences().hideSequence(seq[i]); - } - hasHiddenRows = true; - firePropertyChange("alignment", null, alignment.getSequences()); - } - } - - public void showSequence(int index) - { - Vector tmp = alignment.getHiddenSequences().showSequence(index, - hiddenRepSequences); - if (tmp.size() > 0) - { - if (selectionGroup == null) - { - selectionGroup = new SequenceGroup(); - selectionGroup.setEndRes(alignment.getWidth() - 1); - } - - for (int t = 0; t < tmp.size(); t++) - { - selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false); - } - firePropertyChange("alignment", null, alignment.getSequences()); - sendSelection(); - } - - if (alignment.getHiddenSequences().getSize() < 1) - { - hasHiddenRows = false; - } - } - - public void showColumn(int col) - { - colSel.revealHiddenColumns(col); - if (colSel.getHiddenColumns() == null) - { - hasHiddenColumns = false; - } - } - - public void showAllHiddenColumns() - { - colSel.revealAllHiddenColumns(); - hasHiddenColumns = false; - } - - public void showAllHiddenSeqs() - { - if (alignment.getHiddenSequences().getSize() > 0) - { - if (selectionGroup == null) - { - selectionGroup = new SequenceGroup(); - selectionGroup.setEndRes(alignment.getWidth() - 1); - } - Vector tmp = alignment.getHiddenSequences().showAll( - hiddenRepSequences); - for (int t = 0; t < tmp.size(); t++) - { - selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false); - } - firePropertyChange("alignment", null, alignment.getSequences()); - sendSelection(); - hasHiddenRows = false; - hiddenRepSequences = null; - } - } - - public void invertColumnSelection() - { - colSel.invertColumnSelection(0, alignment.getWidth()); - } - - public int adjustForHiddenSeqs(int alignmentIndex) - { - return alignment.getHiddenSequences().adjustForHiddenSeqs( - alignmentIndex); - } - - /** - * This method returns an array of new SequenceI objects derived from the - * whole alignment or just the current selection with start and end points - * adjusted - * - * @note if you need references to the actual SequenceI objects in the - * alignment or currently selected then use getSequenceSelection() - * @return selection as new sequenceI objects - */ - public SequenceI[] getSelectionAsNewSequence() - { - SequenceI[] sequences; - - if (selectionGroup == null) - { - sequences = alignment.getSequencesArray(); - AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation(); - for (int i = 0; i < sequences.length; i++) - { - sequences[i] = new Sequence(sequences[i], annots); // construct new - // sequence with - // subset of visible - // annotation - } - } - else - { - sequences = selectionGroup.getSelectionAsNewSequences(alignment); - } - - return sequences; - } - - /** - * get the currently selected sequence objects or all the sequences in the - * alignment. - * - * @return array of references to sequence objects - */ - public SequenceI[] getSequenceSelection() - { - SequenceI[] sequences = null; - if (selectionGroup != null) - { - sequences = selectionGroup.getSequencesInOrder(alignment); - } - if (sequences == null) - { - sequences = alignment.getSequencesArray(); - } - return sequences; - } - - /** - * This method returns the visible alignment as text, as seen on the GUI, ie - * if columns are hidden they will not be returned in the result. Use this for - * calculating trees, PCA, redundancy etc on views which contain hidden - * columns. - * - * @return String[] - */ - public jalview.datamodel.CigarArray getViewAsCigars( - boolean selectedRegionOnly) - { - return new jalview.datamodel.CigarArray(alignment, (hasHiddenColumns ? colSel : null), (selectedRegionOnly ? selectionGroup : null)); - } - - /** - * 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); - } - - /** - * 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 - * @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 - */ - public jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly, boolean markGroups) - { - return new AlignmentView(alignment, colSel, selectionGroup, hasHiddenColumns, selectedOnly, markGroups); - } - - /** - * This method returns the visible alignment as text, as seen on the GUI, ie - * if columns are hidden they will not be returned in the result. Use this for - * calculating trees, PCA, redundancy etc on views which contain hidden - * columns. - * - * @return String[] - */ - public String[] getViewAsString(boolean selectedRegionOnly) - { - String[] 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() + 1; - } - else - { - iSize = alignment.getHeight(); - seqs = alignment.getSequencesArray(); - end = alignment.getWidth(); - } - selection = new String[iSize]; - if (hasHiddenColumns) - { - selection = colSel.getVisibleSequenceStrings(start, end, seqs); - } - else - { - for (i = 0; i < iSize; i++) - { - selection[i] = seqs[i].getSequenceAsString(start, end); - } - - } - return selection; - } - - public int[][] getVisibleRegionBoundaries(int min, int max) - { - Vector regions = new Vector(); - int start = min; - int end = max; - - do - { - if (hasHiddenColumns) - { - if (start == 0) - { - start = colSel.adjustForHiddenColumns(start); - } - - end = colSel.getHiddenBoundaryRight(start); - if (start == end) - { - end = max; - } - if (end > max) - { - end = max; - } - } - - regions.addElement(new int[] - { start, end }); - - if (hasHiddenColumns) - { - start = colSel.adjustForHiddenColumns(end); - start = colSel.getHiddenBoundaryLeft(start) + 1; - } - } while (end < max); - - int[][] startEnd = new int[regions.size()][2]; - - regions.copyInto(startEnd); - - return startEnd; - - } public boolean getShowHiddenMarkers() { @@ -1692,109 +1098,6 @@ public class AlignViewport implements SelectionSource, VamsasSource showHiddenMarkers = show; } - public String getSequenceSetId() - { - if (sequenceSetID == null) - { - sequenceSetID = alignment.hashCode() + ""; - } - - return sequenceSetID; - } - - /** - * unique viewId for synchronizing state with stored Jalview Project - * - */ - private String viewId = null; - - public String getViewId() - { - if (viewId == null) - { - viewId = this.getSequenceSetId() + "." + this.hashCode() + ""; - } - return viewId; - } - - public void alignmentChanged(AlignmentPanel ap) - { - if (padGaps) - { - alignment.padGaps(); - } - if (hconsensus != null && autoCalculateConsensus) - { - updateConservation(ap); - } - if (autoCalculateConsensus) - { - updateConsensus(ap); - } - - // Reset endRes of groups if beyond alignment width - int alWidth = alignment.getWidth(); - Vector groups = alignment.getGroups(); - if (groups != null) - { - for (int i = 0; i < groups.size(); i++) - { - SequenceGroup sg = (SequenceGroup) groups.elementAt(i); - if (sg.getEndRes() > alWidth) - { - sg.setEndRes(alWidth - 1); - } - } - } - - if (selectionGroup != null && selectionGroup.getEndRes() > alWidth) - { - selectionGroup.setEndRes(alWidth - 1); - } - - resetAllColourSchemes(); - - // alignment.adjustSequenceAnnotations(); - } - - void resetAllColourSchemes() - { - ColourSchemeI cs = globalColourScheme; - if (cs != null) - { - if (cs instanceof ClustalxColourScheme) - { - ((ClustalxColourScheme) cs).resetClustalX(alignment.getSequences(), - alignment.getWidth()); - } - - cs.setConsensus(hconsensus); - if (cs.conservationApplied()) - { - Alignment al = (Alignment) alignment; - Conservation c = new Conservation("All", - ResidueProperties.propHash, 3, al.getSequences(), 0, - al.getWidth() - 1); - c.calculate(); - c.verdict(false, ConsPercGaps); - - cs.setConservation(c); - } - } - - int s, sSize = alignment.getGroups().size(); - for (s = 0; s < sSize; s++) - { - SequenceGroup sg = (SequenceGroup) alignment.getGroups().elementAt(s); - if (sg.cs != null && sg.cs instanceof ClustalxColourScheme) - { - ((ClustalxColourScheme) sg.cs).resetClustalX( - sg.getSequences(hiddenRepSequences), sg.getWidth()); - } - sg.recalcConservation(); - } - } - public Color getSequenceColour(SequenceI seq) { if (sequenceColours == null || !sequenceColours.containsKey(seq)) @@ -1916,7 +1219,7 @@ public class AlignViewport implements SelectionSource, VamsasSource SequenceGroup sg = (SequenceGroup) groups.elementAt(ig); if (sg.idColour != null) { - Vector sqs = sg.getSequences(hiddenRepSequences); + Vector sqs = sg.getSequences(getHiddenRepSequences()); for (int s = 0, sSize = sqs.size(); s < sSize; s++) { sequenceColours.put(sqs.elementAt(s), sg.idColour); @@ -2007,48 +1310,12 @@ public class AlignViewport implements SelectionSource, VamsasSource return followSelection; } - private long sgrouphash = -1, colselhash = -1; - boolean showSeqFeaturesHeight; - /** - * checks current SelectionGroup against record of last hash value, and - * updates record. - * - * @return true if SelectionGroup changed since last call - */ - boolean isSelectionGroupChanged() - { - int hc = (selectionGroup == null) ? -1 : selectionGroup.hashCode(); - if (hc != sgrouphash) - { - sgrouphash = hc; - return true; - } - return false; - } - - /** - * checks current colsel against record of last hash value, and updates - * record. - * - * @return true if colsel changed since last call - */ - boolean isColSelChanged() - { - int hc = (colSel == null) ? -1 : colSel.hashCode(); - if (hc != colselhash) - { - colselhash = hc; - return true; - } - return false; - } - public void sendSelection() { jalview.structure.StructureSelectionManager - .getStructureSelectionManager().sendSelection( + .getStructureSelectionManager(Desktop.instance).sendSelection( new SequenceGroup(getSelectionGroup()), new ColumnSelection(getColumnSelection()), this); } @@ -2063,18 +1330,6 @@ public class AlignViewport implements SelectionSource, VamsasSource return showSeqFeaturesHeight; } - boolean showUnconserved = false; - - public boolean getShowUnconserved() - { - return showUnconserved; - } - - public void setShowUnconserved(boolean showunconserved) - { - showUnconserved = showunconserved; - } - /** * return the alignPanel containing the given viewport. Use this to get the * components currently handling the given viewport. @@ -2109,106 +1364,6 @@ public class AlignViewport implements SelectionSource, VamsasSource } /** - * should conservation rows be shown for groups - */ - boolean showGroupConservation = false; - - /** - * should consensus rows be shown for groups - */ - boolean showGroupConsensus = false; - - /** - * should consensus profile be rendered by default - */ - public boolean showSequenceLogo = false; - - /** - * should consensus histograms be rendered by default - */ - public boolean showConsensusHistogram = true; - - /** - * @return the showConsensusProfile - */ - public boolean isShowSequenceLogo() - { - return showSequenceLogo; - } - - /** - * @param showSequenceLogo - * the new value - */ - 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(); - } - } - this.showSequenceLogo = showSequenceLogo; - } - - /** - * @param showConsensusHistogram - * the showConsensusHistogram to set - */ - public void setShowConsensusHistogram(boolean showConsensusHistogram) - { - this.showConsensusHistogram = showConsensusHistogram; - } - - /** - * @return the showGroupConservation - */ - public boolean isShowGroupConservation() - { - return showGroupConservation; - } - - /** - * @param showGroupConservation - * the showGroupConservation to set - */ - public void setShowGroupConservation(boolean showGroupConservation) - { - this.showGroupConservation = showGroupConservation; - } - - /** - * @return the showGroupConsensus - */ - public boolean isShowGroupConsensus() - { - return showGroupConsensus; - } - - /** - * @param showGroupConsensus - * the showGroupConsensus to set - */ - public void setShowGroupConsensus(boolean showGroupConsensus) - { - this.showGroupConsensus = showGroupConsensus; - } - - /** - * - * @return flag to indicate if the consensus histogram should be rendered by - * default - */ - public boolean isShowConsensusHistogram() - { - return this.showConsensusHistogram; - } - - /** * synthesize a column selection if none exists so it covers the given * selection group. if wholewidth is false, no column selection is made if the * selection group covers the whole alignment width. @@ -2240,4 +1395,67 @@ 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()][]); + } + + + public boolean isNormaliseSequenceLogo() + { + return normaliseSequenceLogo; + } + + public void setNormaliseSequenceLogo(boolean state) + { + normaliseSequenceLogo = state; + } + + + /** + * + * @return true if alignment characters should be displayed + */ + public boolean isValidCharWidth() + { + return validCharWidth; + } }