X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=8a95015f483fd8650d55fd8f313d6b3ac2836d7c;hb=1cec732f963ab102c9d8381203df8c8cba2a9ee4;hp=1b39869e87efbd99148501d3faf1d3275fed9e13;hpb=b65330720abd1329eac5fddbed9516b8302abe52;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index 1b39869..eb9c180 100644 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -1,60 +1,66 @@ /* - * 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 + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . - */ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; -import java.util.*; - -import java.awt.*; - -import jalview.analysis.*; -import jalview.api.AlignCalcManagerI; +import jalview.analysis.AlignmentUtils; +import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; -import jalview.api.OOMHandlerI; - -import jalview.bin.*; - -import jalview.datamodel.*; - -import jalview.schemes.*; +import jalview.api.FeatureColourI; +import jalview.api.FeatureSettingsModelI; +import jalview.api.FeaturesDisplayedI; +import jalview.api.ViewStyleI; +import jalview.bin.Cache; +import jalview.commands.CommandI; +import jalview.datamodel.AlignedCodonFrame; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; +import jalview.datamodel.SearchResults; +import jalview.datamodel.SearchResultsI; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.renderer.ResidueShader; +import jalview.schemes.ColourSchemeI; +import jalview.schemes.ColourSchemeProperty; +import jalview.schemes.ResidueColourScheme; +import jalview.schemes.UserColourScheme; import jalview.structure.SelectionSource; import jalview.structure.StructureSelectionManager; import jalview.structure.VamsasSource; -import jalview.workers.AlignCalcManager; -import jalview.workers.ConservationThread; +import jalview.util.MessageManager; +import jalview.viewmodel.AlignmentViewport; +import jalview.ws.params.AutoCalcSetting; + +import java.awt.Container; +import java.awt.Dimension; +import java.awt.Font; +import java.awt.FontMetrics; +import java.awt.Rectangle; +import java.util.Hashtable; +import java.util.Iterator; +import java.util.List; + +import javax.swing.JInternalFrame; /** * DOCUMENT ME! @@ -62,144 +68,29 @@ import jalview.workers.ConservationThread; * @author $author$ * @version $Revision: 1.141 $ */ -public class AlignViewport extends AlignmentViewport implements SelectionSource, VamsasSource, AlignViewportI +public class AlignViewport extends AlignmentViewport + implements SelectionSource { - private static final int RIGHT_JUSTIFY = 1; - - int startRes; - - int endRes; - - int startSeq; - - int endSeq; - - boolean showJVSuffix = true; - - boolean showText = true; - - boolean showColourText = false; - - boolean showBoxes = true; - - boolean wrapAlignment = false; - - boolean renderGaps = true; - - boolean showSequenceFeatures = false; - - boolean showAnnotation = true; - - boolean colourAppliesToAllGroups = true; - - ColourSchemeI globalColourScheme = null; - - boolean conservationColourSelected = false; - - boolean abovePIDThreshold = false; - - SequenceGroup selectionGroup; - - int charHeight; - - int charWidth; - - boolean validCharWidth; - - int wrappedWidth; - Font font; - boolean seqNameItalics; - - AlignmentI alignment; - - ColumnSelection colSel = new ColumnSelection(); - - int threshold; - - int increment; - - NJTree currentTree = null; - - boolean scaleAboveWrapped = false; - - boolean scaleLeftWrapped = true; - - boolean scaleRightWrapped = true; - - boolean hasHiddenColumns = false; - - boolean hasHiddenRows = false; - - boolean showHiddenMarkers = true; - boolean cursorMode = false; - /** - * Keys are the feature types which are currently visible. Note: Values are - * not used! - */ - Hashtable featuresDisplayed = null; - - /** DOCUMENT ME!! */ - public Hashtable[] hconsensus; - - public Hashtable[] hStrucConsensus; - - AlignmentAnnotation consensus; - - AlignmentAnnotation strucConsensus; - - AlignmentAnnotation conservation; - - AlignmentAnnotation quality; - - AlignmentAnnotation[] groupConsensus; - - AlignmentAnnotation[] groupConservation; - - boolean autoCalculateConsensus = true; - - boolean autoCalculateStrucConsensus = true; - - // 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; + private Rectangle explodedGeometry; - String viewName; + private String viewName; - String sequenceSetID; - - boolean gatherViewsHere = false; - - Stack historyList = new Stack(); - - Stack redoList = new Stack(); - - Hashtable sequenceColours; - - int thresholdTextColour = 0; - - Color textColour = Color.black; - - Color textColour2 = Color.white; - - boolean rightAlignIds = false; - - Hashtable hiddenRepSequences; + /* + * Flag set true on the view that should 'gather' multiple views of the same + * sequence set id when a project is reloaded. Set false on all views when + * they are 'exploded' into separate windows. Set true on the current view + * when 'Gather' is performed, and also on the first tab when the first new + * view is created. + */ + private boolean gatherViewsHere = false; - boolean sortByTree; + private AnnotationColumnChooser annotationColumnSelectionState; /** * Creates a new AlignViewport object. @@ -209,7 +100,7 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource, */ public AlignViewport(AlignmentI al) { - setAlignment(al); + super(al); init(); } @@ -227,20 +118,21 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource, public AlignViewport(AlignmentI al, String seqsetid, String viewid) { + super(al); sequenceSetID = seqsetid; viewId = viewid; // TODO remove these once 2.4.VAMSAS release finished if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null) { - Cache.log.debug("Setting viewport's sequence set id : " - + sequenceSetID); + Cache.log.debug( + "Setting viewport's sequence set id : " + sequenceSetID); } if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null) { Cache.log.debug("Setting viewport's view id : " + viewId); } - setAlignment(al); init(); + } /** @@ -251,21 +143,12 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource, * @param hiddenColumns * ColumnSelection */ - public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns) + public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns) { - setAlignment(al); + super(al); if (hiddenColumns != null) { - this.colSel = hiddenColumns; - if (hiddenColumns.getHiddenColumns() != null - && hiddenColumns.getHiddenColumns().size() > 0) - { - hasHiddenColumns = true; - } - else - { - hasHiddenColumns = false; - } + al.setHiddenColumns(hiddenColumns); } init(); } @@ -278,7 +161,7 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource, * @param seqsetid * (may be null) */ - public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns, + public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns, String seqsetid) { this(al, hiddenColumns, seqsetid, null); @@ -294,63 +177,72 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource, * @param viewid * (may be null) */ - public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns, + public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns, String seqsetid, String viewid) { + super(al); sequenceSetID = seqsetid; viewId = viewid; // TODO remove these once 2.4.VAMSAS release finished if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null) { - Cache.log.debug("Setting viewport's sequence set id : " - + sequenceSetID); + Cache.log.debug( + "Setting viewport's sequence set id : " + sequenceSetID); } if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null) { Cache.log.debug("Setting viewport's view id : " + viewId); } - setAlignment(al); + if (hiddenColumns != null) { - this.colSel = hiddenColumns; - if (hiddenColumns.getHiddenColumns() != null - && hiddenColumns.getHiddenColumns().size() > 0) - { - hasHiddenColumns = true; - } - else - { - hasHiddenColumns = false; - } + al.setHiddenColumns(hiddenColumns); } init(); } - void init() + /** + * Apply any settings saved in user preferences + */ + private void applyViewProperties() { - this.startRes = 0; - this.endRes = alignment.getWidth() - 1; - this.startSeq = 0; - this.endSeq = alignment.getHeight() - 1; - - antiAlias = Cache.getDefault("ANTI_ALIAS", false); + antiAlias = Cache.getDefault(Preferences.ANTI_ALIAS, false); - showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true); - showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true); + viewStyle.setShowJVSuffix( + Cache.getDefault(Preferences.SHOW_JVSUFFIX, true)); + setShowAnnotation(Cache.getDefault(Preferences.SHOW_ANNOTATIONS, true)); - rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false); - centreColumnLabels = Cache.getDefault("CENTRE_COLUMN_LABELS", false); - autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true); + setRightAlignIds(Cache.getDefault(Preferences.RIGHT_ALIGN_IDS, false)); + setCentreColumnLabels(Cache.getDefault(Preferences.CENTRE_COLUMN_LABELS, false)); + autoCalculateConsensusAndConservation = Cache.getDefault(Preferences.AUTO_CALC_CONSENSUS, true); - padGaps = Cache.getDefault("PAD_GAPS", true); - shownpfeats = Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true); - showdbrefs = Cache.getDefault("SHOW_DBREFS_TOOLTIP", true); + setPadGaps(Cache.getDefault(Preferences.PAD_GAPS, true)); + setShowNPFeats(Cache.getDefault(Preferences.SHOW_NPFEATS_TOOLTIP, true)); + setShowDBRefs(Cache.getDefault(Preferences.SHOW_DBREFS_TOOLTIP, true)); + viewStyle.setSeqNameItalics(Cache.getDefault(Preferences.ID_ITALICS, true)); + viewStyle.setWrapAlignment( + Cache.getDefault(Preferences.WRAP_ALIGNMENT, false)); + viewStyle.setShowUnconserved( + Cache.getDefault(Preferences.SHOW_UNCONSERVED, false)); + sortByTree = Cache.getDefault(Preferences.SORT_BY_TREE, false); + followSelection = Cache.getDefault(Preferences.FOLLOW_SELECTIONS, true); + sortAnnotationsBy = SequenceAnnotationOrder + .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS, + SequenceAnnotationOrder.NONE.name())); + showAutocalculatedAbove = Cache + .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false); + viewStyle.setScaleProteinAsCdna( + Cache.getDefault(Preferences.SCALE_PROTEIN_TO_CDNA, true)); + } - String fontName = Cache.getDefault("FONT_NAME", "SansSerif"); - String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + ""); - String fontSize = Cache.getDefault("FONT_SIZE", "10"); + void init() + { + applyViewProperties(); - seqNameItalics = Cache.getDefault("ID_ITALICS", true); + String fontName = Cache.getDefault(Preferences.FONT_NAME, "SansSerif"); + String fontStyle = Cache.getDefault(Preferences.FONT_STYLE, + Font.PLAIN + ""); + String fontSize = Cache.getDefault(Preferences.FONT_SIZE, "10"); int style = 0; @@ -363,10 +255,11 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource, style = 2; } - setFont(new Font(fontName, style, Integer.parseInt(fontSize))); + setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true); alignment - .setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0)); + .setGapCharacter(Cache.getDefault(Preferences.GAP_SYMBOL, "-") + .charAt(0)); // We must set conservation and consensus before setting colour, // as Blosum and Clustal require this to be done @@ -374,2178 +267,828 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource, { if (!alignment.isNucleotide()) { - conservation = new AlignmentAnnotation("Conservation", - "Conservation of total alignment less than " + getConsPercGaps() - + "% gaps", new Annotation[1], 0f, 11f, - AlignmentAnnotation.BAR_GRAPH); - conservation.hasText = true; - conservation.autoCalculated = true; - - if (Cache.getDefault("SHOW_CONSERVATION", true)) - { - alignment.addAnnotation(conservation); - } - - if (Cache.getDefault("SHOW_QUALITY", true)) - { - quality = new AlignmentAnnotation("Quality", - "Alignment Quality based on Blosum62 scores", - new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH); - quality.hasText = true; - quality.autoCalculated = true; - - alignment.addAnnotation(quality); - } - showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION", - false); - - { - - } - } - 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 - // specific alignment - consensus = new AlignmentAnnotation("Consensus", "PID", - new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); - 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); - } + showConservation = Cache.getDefault(Preferences.SHOW_CONSERVATION, + true); + showQuality = Cache.getDefault(Preferences.SHOW_QUALITY, true); + showGroupConservation = Cache + .getDefault(Preferences.SHOW_GROUP_CONSERVATION, false); } + showConsensusHistogram = Cache + .getDefault(Preferences.SHOW_CONSENSUS_HISTOGRAM, true); + showSequenceLogo = Cache.getDefault(Preferences.SHOW_CONSENSUS_LOGO, + false); - } + normaliseSequenceLogo = Cache + .getDefault(Preferences.NORMALISE_CONSENSUS_LOGO, false); + showGroupConsensus = Cache + .getDefault(Preferences.SHOW_GROUP_CONSENSUS, false); + showConsensus = Cache.getDefault(Preferences.SHOW_IDENTITY, true); - if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null) + showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true); + } + initAutoAnnotation(); + String colourProperty = alignment.isNucleotide() + ? Preferences.DEFAULT_COLOUR_NUC + : Preferences.DEFAULT_COLOUR_PROT; + String schemeName = Cache.getProperty(colourProperty); + if (schemeName == null) { - globalColourScheme = ColourSchemeProperty.getColour(alignment, - jalview.bin.Cache.getProperty("DEFAULT_COLOUR")); - - if (globalColourScheme instanceof UserColourScheme) - { - globalColourScheme = UserDefinedColours.loadDefaultColours(); - ((UserColourScheme) globalColourScheme).setThreshold(0, - getIgnoreGapsConsensus()); - } + // only DEFAULT_COLOUR available in Jalview before 2.9 + schemeName = Cache.getDefault(Preferences.DEFAULT_COLOUR, + ResidueColourScheme.NONE); + } + ColourSchemeI colourScheme = ColourSchemeProperty.getColourScheme(this, + alignment, schemeName); + residueShading = new ResidueShader(colourScheme); - if (globalColourScheme != null) - { - globalColourScheme.setConsensus(hconsensus); - } + if (colourScheme instanceof UserColourScheme) + { + residueShading = new ResidueShader( + UserDefinedColours.loadDefaultColours()); + residueShading.setThreshold(0, isIgnoreGapsConsensus()); } - wrapAlignment = jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false); - 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); + if (residueShading != null) + { + residueShading.setConsensus(hconsensus); + } + setColourAppliesToAllGroups(true); } + boolean validCharWidth; + /** - * set the flag - * - * @param b - * features are displayed if true + * {@inheritDoc} */ - public void setShowSequenceFeatures(boolean b) - { - showSequenceFeatures = b; - } - - public boolean getShowSequenceFeatures() + @Override + public void setFont(Font f, boolean setGrid) { - return showSequenceFeatures; - } - - AlignCalcManagerI calculator=new AlignCalcManager(); - - ConsensusThread consensusThread; - - StrucConsensusThread strucConsensusThread; - - boolean consUpdateNeeded = false; - - static boolean UPDATING_CONSENSUS = false; - - static boolean UPDATING_STRUC_CONSENSUS = false; + font = f; - static boolean UPDATING_CONSERVATION = false; + Container c = new Container(); - boolean updatingConsensus = false; + if (setGrid) + { + FontMetrics fm = c.getFontMetrics(font); + int ww = fm.charWidth('M'); + setCharHeight(fm.getHeight()); + setCharWidth(ww); + } + viewStyle.setFontName(font.getName()); + viewStyle.setFontStyle(font.getStyle()); + viewStyle.setFontSize(font.getSize()); - boolean updatingStrucConsensus = false; + validCharWidth = true; + } - boolean updatingConservation = false; + @Override + public void setViewStyle(ViewStyleI settingsForView) + { + super.setViewStyle(settingsForView); + setFont(new Font(viewStyle.getFontName(), viewStyle.getFontStyle(), + viewStyle.getFontSize()), false); + } /** - * centre columnar annotation labels in displayed alignment annotation TODO: - * add to jalviewXML and annotation display settings + * DOCUMENT ME! + * + * @return DOCUMENT ME! */ - boolean centreColumnLabels = false; - - private boolean showdbrefs; - - private boolean shownpfeats; + public Font getFont() + { + return font; + } /** - * trigger update of conservation annotation + * DOCUMENT ME! + * + * @param align + * DOCUMENT ME! */ - public void updateConservation(final AlignmentViewPanel ap) + @Override + public void setAlignment(AlignmentI align) { - // see note in mantis : issue number 8585 - if (alignment.isNucleotide() || conservation == null - || !autoCalculateConsensus) - { - return; - } - - calculator.startWorker(new jalview.workers.ConservationThread(this, ap)); + replaceMappings(align); + super.setAlignment(align); } /** - * trigger update of consensus annotation + * Replace any codon mappings for this viewport with those for the given + * viewport + * + * @param align */ - public void updateConsensus(final AlignmentPanel ap) + public void replaceMappings(AlignmentI align) { - // see note in mantis : issue number 8585 - if (consensus == null || !autoCalculateConsensus) + + /* + * Deregister current mappings (if any) + */ + deregisterMappings(); + + /* + * Register new mappings (if any) + */ + if (align != null) { - return; + Desktop.getInstance().getStructureSelectionManager() + .registerMappings(align.getCodonFrames()); } - consensusThread = new ConsensusThread(ap); - consensusThread.start(); - } - class ConsensusThread extends Thread - { - AlignmentViewPanel ap; - public ConsensusThread(AlignmentPanel ap) + /* + * replace mappings on our alignment + */ + if (alignment != null && align != null) { - this.ap = ap; + alignment.setCodonFrames(align.getCodonFrames()); } + } - public void run() + protected void deregisterMappings() + { + AlignmentI al = getAlignment(); + if (al != null) { - updatingConsensus = true; - while (UPDATING_CONSENSUS) + List mappings = al.getCodonFrames(); + if (mappings != null) { - try + StructureSelectionManager ssm = Desktop.getInstance() + .getStructureSelectionManager(); + for (AlignedCodonFrame acf : mappings) { - if (ap != null) + if (noReferencesTo(acf)) { - ap.paintAlignment(false); + ssm.deregisterMapping(acf); } - - 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; - ap.raiseOOMWarning("calculating consensus", error); - } - UPDATING_CONSENSUS = false; - updatingConsensus = false; + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + @Override + public char getGapCharacter() + { + return getAlignment().getGapCharacter(); + } - if (ap != null) - { - ap.paintAlignment(true); - } + /** + * DOCUMENT ME! + * + * @param gap + * DOCUMENT ME! + */ + public void setGapCharacter(char gap) + { + if (getAlignment() != null) + { + getAlignment().setGapCharacter(gap); } + } - /** - * update the consensus annotation from the sequence profile data using - * current visualization settings. - */ - public void updateAnnotation() + /** + * returns the visible column regions of the alignment + * + * @param selectedRegionOnly + * true to just return the contigs intersecting with the selected + * area + * @return + */ + public Iterator getViewAsVisibleContigs(boolean selectedRegionOnly) + { + int start = 0; + int end = 0; + if (selectedRegionOnly && selectionGroup != null) { - updateAnnotation(false); + start = selectionGroup.getStartRes(); + end = selectionGroup.getEndRes() + 1; } - - protected void updateAnnotation(boolean immediate) + else { - // 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 = alignment.getWidth(); } + return (alignment.getHiddenColumns().getVisContigsIterator(start, end, + false)); } - // --------START Structure Conservation - public void updateStrucConsensus(final AlignmentPanel ap) + /** + * get hash of undo and redo list for the alignment + * + * @return long[] { historyList.hashCode, redoList.hashCode }; + */ + public long[] getUndoRedoHash() { - // see note in mantis : issue number 8585 - if (strucConsensus == null || !autoCalculateStrucConsensus) + // TODO: JAL-1126 + if (historyList == null || redoList == null) { - return; + return new long[] { -1, -1 }; } - strucConsensusThread = new StrucConsensusThread(ap); - strucConsensusThread.start(); + return new long[] { historyList.hashCode(), this.redoList.hashCode() }; } - class StrucConsensusThread extends Thread + /** + * test if a particular set of hashcodes are different to the hashcodes for + * the undo and redo list. + * + * @param undoredo + * the stored set of hashcodes as returned by getUndoRedoHash + * @return true if the hashcodes differ (ie the alignment has been edited) or + * the stored hashcode array differs in size + */ + public boolean isUndoRedoHashModified(long[] undoredo) { - AlignmentPanel ap; - - public StrucConsensusThread(AlignmentPanel ap) + if (undoredo == null) { - this.ap = ap; + return true; + } + long[] cstate = getUndoRedoHash(); + if (cstate.length != undoredo.length) + { + return true; } - public void run() + for (int i = 0; i < cstate.length; i++) { - updatingStrucConsensus = true; - while (UPDATING_STRUC_CONSENSUS) + if (cstate[i] != undoredo[i]) { - 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. - * - * @return consensus sequence as a new sequence object - */ - public SequenceI getConsensusSeq() - { - if (consensus == null) - { - updateConsensus(null); - } - if (consensus == null) - { - return null; - } - StringBuffer seqs = new StringBuffer(); - for (int i = 0; i < consensus.annotations.length; i++) - { - if (consensus.annotations[i] != null) - { - if (consensus.annotations[i].description.charAt(0) == '[') - { - seqs.append(consensus.annotations[i].description.charAt(1)); - } - else - { - seqs.append(consensus.annotations[i].displayCharacter); - } - } - } - - SequenceI sq = new Sequence("Consensus", seqs.toString()); - sq.setDescription("Percentage Identity Consensus " - + ((ignoreGapsInConsensusCalculation) ? " without gaps" : "")); - 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() - { - return conservationColourSelected; - } - - /** - * GUI state - * - * @param b - * enable conservation based shading - */ - public void setConservationSelected(boolean b) - { - conservationColourSelected = b; - } - - /** - * GUI state - * - * @return true if percent identity threshold is applied to shading - */ - public boolean getAbovePIDThreshold() - { - return abovePIDThreshold; - } - - /** - * GUI state - * - * - * @param b - * indicate if percent identity threshold is applied to shading - */ - public void setAbovePIDThreshold(boolean b) - { - abovePIDThreshold = b; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getStartRes() - { - return startRes; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getEndRes() - { - return endRes; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getStartSeq() - { - return startSeq; - } - - /** - * 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! - */ - public void setStartRes(int res) - { - this.startRes = res; - } - - /** - * DOCUMENT ME! - * - * @param seq - * DOCUMENT ME! - */ - public void setStartSeq(int seq) - { - this.startSeq = seq; - } - - /** - * DOCUMENT ME! - * - * @param res - * DOCUMENT ME! - */ - public void setEndRes(int res) - { - if (res > (alignment.getWidth() - 1)) - { - // log.System.out.println(" Corrected res from " + res + " to maximum " + - // (alignment.getWidth()-1)); - res = alignment.getWidth() - 1; - } - - if (res < 0) - { - res = 0; - } - - this.endRes = res; - } - - /** - * DOCUMENT ME! - * - * @param seq - * DOCUMENT ME! - */ - public void setEndSeq(int seq) - { - if (seq > alignment.getHeight()) - { - seq = alignment.getHeight(); - } - - if (seq < 0) - { - seq = 0; - } - - this.endSeq = seq; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getEndSeq() - { - return endSeq; - } - - /** - * DOCUMENT ME! - * - * @param f - * DOCUMENT ME! - */ - public void setFont(Font f) - { - font = f; - - Container c = new Container(); - - java.awt.FontMetrics fm = c.getFontMetrics(font); - setCharHeight(fm.getHeight()); - setCharWidth(fm.charWidth('M')); - validCharWidth = true; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public Font getFont() - { - return font; - } - - /** - * DOCUMENT ME! - * - * @param w - * DOCUMENT ME! - */ - public void setCharWidth(int w) - { - this.charWidth = w; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getCharWidth() - { - return charWidth; - } - - /** - * DOCUMENT ME! - * - * @param h - * DOCUMENT ME! - */ - public void setCharHeight(int h) - { - this.charHeight = h; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getCharHeight() - { - return charHeight; - } - - /** - * DOCUMENT ME! - * - * @param w - * DOCUMENT ME! - */ - public void setWrappedWidth(int w) - { - this.wrappedWidth = w; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getWrappedWidth() - { - return wrappedWidth; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public AlignmentI getAlignment() - { - return alignment; - } - - /** - * DOCUMENT ME! - * - * @param align - * DOCUMENT ME! - */ - public void setAlignment(AlignmentI align) - { - if (alignment != null && alignment.getCodonFrames() != null) - { - StructureSelectionManager.getStructureSelectionManager( - Desktop.instance).removeMappings(alignment.getCodonFrames()); - } - this.alignment = align; - if (alignment.getCodonFrames() != null) - { - StructureSelectionManager.getStructureSelectionManager( - Desktop.instance).addMappings(alignment.getCodonFrames()); - } - } - - /** - * DOCUMENT ME! - * - * @param state - * DOCUMENT ME! - */ - public void setWrapAlignment(boolean state) - { - wrapAlignment = state; - } - - /** - * DOCUMENT ME! - * - * @param state - * DOCUMENT ME! - */ - public void setShowText(boolean state) - { - showText = state; - } - - /** - * DOCUMENT ME! - * - * @param state - * DOCUMENT ME! - */ - public void setRenderGaps(boolean state) - { - renderGaps = state; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getColourText() - { - return showColourText; - } - - /** - * DOCUMENT ME! - * - * @param state - * DOCUMENT ME! - */ - public void setColourText(boolean state) - { - showColourText = state; - } - - /** - * DOCUMENT ME! - * - * @param state - * DOCUMENT ME! - */ - public void setShowBoxes(boolean state) - { - showBoxes = state; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getWrapAlignment() - { - return wrapAlignment; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getShowText() - { - return showText; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getShowBoxes() - { - return showBoxes; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public char getGapCharacter() - { - return getAlignment().getGapCharacter(); - } - - /** - * DOCUMENT ME! - * - * @param gap - * DOCUMENT ME! - */ - public void setGapCharacter(char gap) - { - if (getAlignment() != null) - { - getAlignment().setGapCharacter(gap); - } - } - - /** - * DOCUMENT ME! - * - * @param thresh - * DOCUMENT ME! - */ - public void setThreshold(int thresh) - { - threshold = thresh; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getThreshold() - { - return threshold; - } - - /** - * DOCUMENT ME! - * - * @param inc - * DOCUMENT ME! - */ - public void setIncrement(int inc) - { - increment = inc; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getIncrement() - { - return increment; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public ColumnSelection getColumnSelection() - { - return colSel; - } - - /** - * DOCUMENT ME! - * - * @param tree - * DOCUMENT ME! - */ - public void setCurrentTree(NJTree tree) - { - currentTree = tree; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public NJTree getCurrentTree() - { - return currentTree; - } - - /** - * DOCUMENT ME! - * - * @param b - * DOCUMENT ME! - */ - public void setColourAppliesToAllGroups(boolean b) - { - colourAppliesToAllGroups = b; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getColourAppliesToAllGroups() - { - return colourAppliesToAllGroups; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getShowJVSuffix() - { - return showJVSuffix; - } - - /** - * DOCUMENT ME! - * - * @param b - * DOCUMENT ME! - */ - public void setShowJVSuffix(boolean b) - { - showJVSuffix = b; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getShowAnnotation() - { - return showAnnotation; - } - - /** - * DOCUMENT ME! - * - * @param b - * DOCUMENT ME! - */ - public void setShowAnnotation(boolean b) - { - showAnnotation = b; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getScaleAboveWrapped() - { - return scaleAboveWrapped; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getScaleLeftWrapped() - { - return scaleLeftWrapped; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getScaleRightWrapped() - { - return scaleRightWrapped; - } - - /** - * DOCUMENT ME! - * - * @param b - * DOCUMENT ME! - */ - public void setScaleAboveWrapped(boolean b) - { - scaleAboveWrapped = b; - } - - /** - * DOCUMENT ME! - * - * @param b - * DOCUMENT ME! - */ - public void setScaleLeftWrapped(boolean b) - { - scaleLeftWrapped = b; - } - - /** - * DOCUMENT ME! - * - * @param b - * DOCUMENT ME! - */ - public void setScaleRightWrapped(boolean b) - { - 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) - { - isDataset = b; - } - - public boolean isDataset() - { - 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() - { - return showHiddenMarkers; - } - - public void setShowHiddenMarkers(boolean show) - { - 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); - } - if (autoCalculateStrucConsensus) - { - updateStrucConsensus(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()) - { - AlignmentI al = (Alignment) alignment; - Conservation c = new Conservation("All", - ResidueProperties.propHash, 3, al.getSequences(), 0, al - .getWidth() - 1); - c.calculate(); - c.verdict(false, getConsPercGaps()); - - 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)) - { - return Color.white; - } - else - { - return (Color) sequenceColours.get(seq); - } - } - - public void setSequenceColour(SequenceI seq, Color col) - { - if (sequenceColours == null) - { - sequenceColours = new Hashtable(); - } - - if (col == null) - { - sequenceColours.remove(seq); - } - else - { - sequenceColours.put(seq, col); - } - } - - /** - * returns the visible column regions of the alignment - * - * @param selectedRegionOnly - * true to just return the contigs intersecting with the selected - * area - * @return - */ - public int[] getViewAsVisibleContigs(boolean selectedRegionOnly) - { - int[] viscontigs = null; - int start = 0, end = 0; - if (selectedRegionOnly && selectionGroup != null) - { - start = selectionGroup.getStartRes(); - end = selectionGroup.getEndRes() + 1; - } - else - { - end = alignment.getWidth(); - } - viscontigs = colSel.getVisibleContigs(start, end); - return viscontigs; - } - - /** - * get hash of undo and redo list for the alignment - * - * @return long[] { historyList.hashCode, redoList.hashCode }; - */ - public long[] getUndoRedoHash() - { - if (historyList == null || redoList == null) - return new long[] - { -1, -1 }; - return new long[] - { historyList.hashCode(), this.redoList.hashCode() }; - } - - /** - * test if a particular set of hashcodes are different to the hashcodes for - * the undo and redo list. - * - * @param undoredo - * the stored set of hashcodes as returned by getUndoRedoHash - * @return true if the hashcodes differ (ie the alignment has been edited) or - * the stored hashcode array differs in size - */ - public boolean isUndoRedoHashModified(long[] undoredo) - { - if (undoredo == null) - { - return true; - } - long[] cstate = getUndoRedoHash(); - if (cstate.length != undoredo.length) - { - return true; - } - - for (int i = 0; i < cstate.length; i++) - { - if (cstate[i] != undoredo[i]) - { - return true; - } - } - return false; - } - - public boolean getCentreColumnLabels() - { - return centreColumnLabels; - } - - public void setCentreColumnLabels(boolean centrecolumnlabels) - { - centreColumnLabels = centrecolumnlabels; - } - - public void updateSequenceIdColours() - { - Vector groups = alignment.getGroups(); - if (sequenceColours == null) - { - sequenceColours = new Hashtable(); - } - for (int ig = 0, igSize = groups.size(); ig < igSize; ig++) - { - SequenceGroup sg = (SequenceGroup) groups.elementAt(ig); - if (sg.idColour != null) - { - Vector sqs = sg.getSequences(hiddenRepSequences); - for (int s = 0, sSize = sqs.size(); s < sSize; s++) - { - sequenceColours.put(sqs.elementAt(s), sg.idColour); - } + return true; } } + return false; } + public boolean followSelection = true; + /** - * enable or disable the display of Database Cross References in the sequence - * ID tooltip + * @return true if view selection should always follow the selections + * broadcast by other selection sources */ - public void setShowDbRefs(boolean show) + public boolean getFollowSelection() { - showdbrefs = show; + return followSelection; } /** - * - * @return true if Database References are to be displayed on tooltips. + * Send the current selection to be broadcast to any selection listeners. */ - public boolean isShowDbRefs() + @Override + public void sendSelection() { - return showdbrefs; + Desktop.getInstance().getStructureSelectionManager().sendSelection( + new SequenceGroup(getSelectionGroup()), + new ColumnSelection(getColumnSelection()), + new HiddenColumns(getAlignment().getHiddenColumns()), this); } /** + * return the alignPanel containing the given viewport. Use this to get the + * components currently handling the given viewport. * - * @return true if Non-positional features are to be displayed on tooltips. + * @param av + * @return null or an alignPanel guaranteed to have non-null alignFrame + * reference */ - public boolean isShowNpFeats() + public AlignmentPanel getAlignPanel() { - return shownpfeats; + AlignmentPanel[] aps = PaintRefresher + .getAssociatedPanels(this.getSequenceSetId()); + for (int p = 0; aps != null && p < aps.length; p++) + { + if (aps[p].av == this) + { + return aps[p]; + } + } + return null; } - /** - * enable or disable the display of Non-Positional sequence features in the - * sequence ID tooltip - * - * @param show - */ - public void setShowNpFeats(boolean show) + public boolean getSortByTree() { - shownpfeats = show; + return sortByTree; } - /** - * - * @return true if view has hidden rows - */ - public boolean hasHiddenRows() + public void setSortByTree(boolean sort) { - return hasHiddenRows; + sortByTree = sort; } /** - * - * @return true if view has hidden columns + * Returns the (Desktop) instance of the StructureSelectionManager */ - public boolean hasHiddenColumns() + @Override + public StructureSelectionManager getStructureSelectionManager() { - return hasHiddenColumns; + return Desktop.getInstance().getStructureSelectionManager(); } - /** - * when set, view will scroll to show the highlighted position - */ - public boolean followHighlight = true; - - /** - * @return true if view should scroll to show the highlighted region of a - * sequence - * @return - */ - public boolean getFollowHighlight() + @Override + public boolean isNormaliseSequenceLogo() { - return followHighlight; + return normaliseSequenceLogo; } - public boolean followSelection = true; + public void setNormaliseSequenceLogo(boolean state) + { + normaliseSequenceLogo = state; + } /** - * @return true if view selection should always follow the selections - * broadcast by other selection sources + * + * @return true if alignment characters should be displayed */ - public boolean getFollowSelection() + @Override + public boolean isValidCharWidth() { - return followSelection; + return validCharWidth; } - private long sgrouphash = -1, colselhash = -1; + private Hashtable calcIdParams = new Hashtable<>(); - boolean showSeqFeaturesHeight; + public AutoCalcSetting getCalcIdSettingsFor(String calcId) + { + return calcIdParams.get(calcId); + } - /** - * checks current SelectionGroup against record of last hash value, and - * updates record. - * - * @param b - * update the record of last hash value - * - * @return true if SelectionGroup changed since last call (when b is true) - */ - boolean isSelectionGroupChanged(boolean b) + public void setCalcIdSettingsFor(String calcId, AutoCalcSetting settings, + boolean needsUpdate) { - int hc = (selectionGroup == null || selectionGroup.getSize() == 0) ? -1 - : selectionGroup.hashCode(); - if (hc != -1 && hc != sgrouphash) + calcIdParams.put(calcId, settings); + // TODO: create a restart list to trigger any calculations that need to be + // restarted after load + // calculator.getRegisteredWorkersOfClass(settings.getWorkerClass()) + if (needsUpdate) { - if (b) - { - sgrouphash = hc; - } - return true; + Cache.log.debug("trigger update for " + calcId); } - return false; } /** - * checks current colsel against record of last hash value, and optionally - * updates record. + * Method called when another alignment's edit (or possibly other) command is + * broadcast to here. + * + * To allow for sequence mappings (e.g. protein to cDNA), we have to first + * 'unwind' the command on the source sequences (in simulation, not in fact), + * and then for each edit in turn: + *
    + *
  • compute the equivalent edit on the mapped sequences
    • + *
  • apply the mapped edit
    • + *
  • 'apply' the source edit to the working copy of the source + * sequences
    • + *
* - * @param b - * update the record of last hash value - * @return true if colsel changed since last call (when b is true) + * @param command + * @param undo + * @param ssm */ - boolean isColSelChanged(boolean b) + @Override + public void mirrorCommand(CommandI command, boolean undo, + StructureSelectionManager ssm, VamsasSource source) { - int hc = (colSel == null || colSel.size() == 0) ? -1 : colSel - .hashCode(); - if (hc != -1 && hc != colselhash) + /* + * Do nothing unless we are a 'complement' of the source. May replace this + * with direct calls not via SSM. + */ + if (source instanceof AlignViewportI + && ((AlignViewportI) source).getCodingComplement() == this) { - if (b) - { - colselhash = hc; - } - return true; + // ok to continue; + } + else + { + return; } - return false; - } - public void sendSelection() - { - jalview.structure.StructureSelectionManager - .getStructureSelectionManager(Desktop.instance).sendSelection( - new SequenceGroup(getSelectionGroup()), - new ColumnSelection(getColumnSelection()), this); + CommandI mappedCommand = ssm.mapCommand(command, undo, getAlignment(), + getGapCharacter()); + if (mappedCommand != null) + { + AlignmentI[] views = getAlignPanel().alignFrame.getViewAlignments(); + mappedCommand.doCommand(views); + getAlignPanel().alignmentChanged(); + } } - public void setShowSequenceFeaturesHeight(boolean selected) + /** + * Add the sequences from the given alignment to this viewport. Optionally, + * may give the user the option to open a new frame, or split panel, with cDNA + * and protein linked. + * + * @param toAdd + * @param title + */ + public void addAlignment(AlignmentI toAdd, String title) { - showSeqFeaturesHeight = selected; - } + // TODO: promote to AlignViewportI? applet CutAndPasteTransfer is different - public boolean getShowSequenceFeaturesHeight() - { - return showSeqFeaturesHeight; - } + // JBPComment: title is a largely redundant parameter at the moment + // JBPComment: this really should be an 'insert/pre/append' controller + // JBPComment: but the DNA/Protein check makes it a bit more complex - boolean showUnconserved = false; + // refactored from FileLoader / CutAndPasteTransfer / SequenceFetcher with + // this comment: + // TODO: create undo object for this JAL-1101 - public boolean getShowUnconserved() - { - return showUnconserved; - } + /* + * Ensure datasets are created for the new alignment as + * mappings operate on dataset sequences + */ + toAdd.setDataset(null); - public void setShowUnconserved(boolean showunconserved) - { - showUnconserved = showunconserved; + /* + * Check if any added sequence could be the object of a mapping or + * cross-reference; if so, make the mapping explicit + */ + getAlignment().realiseMappings(toAdd.getSequences()); + + /* + * If any cDNA/protein mappings exist or can be made between the alignments, + * offer to open a split frame with linked alignments + */ + if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true)) + { + if (AlignmentUtils.isMappable(toAdd, getAlignment())) + { + openLinkedAlignment(toAdd, title); + return; + } + } + addDataToAlignment(toAdd); } /** - * return the alignPanel containing the given viewport. Use this to get the - * components currently handling the given viewport. + * adds sequences to this alignment * - * @param av - * @return null or an alignPanel guaranteed to have non-null alignFrame - * reference + * @param toAdd */ - public AlignmentPanel getAlignPanel() + void addDataToAlignment(AlignmentI toAdd) { - AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(this - .getSequenceSetId()); - AlignmentPanel ap = null; - for (int p = 0; aps != null && p < aps.length; p++) + // TODO: JAL-407 regardless of above - identical sequences (based on ID and + // provenance) should share the same dataset sequence + + AlignmentI al = getAlignment(); + String gap = String.valueOf(al.getGapCharacter()); + for (int i = 0; i < toAdd.getHeight(); i++) { - if (aps[p].av == this) + SequenceI seq = toAdd.getSequenceAt(i); + /* + * experimental! + * - 'align' any mapped sequences as per existing + * e.g. cdna to genome, domain hit to protein sequence + * very experimental! (need a separate menu option for this) + * - only add mapped sequences ('select targets from a dataset') + */ + if (true /*AlignmentUtils.alignSequenceAs(seq, al, gap, true, true)*/) { - return aps[p]; + al.addSequence(seq); } } - return null; - } - - public boolean getSortByTree() - { - return sortByTree; - } - public void setSortByTree(boolean sort) - { - sortByTree = sort; + ranges.setEndSeq(getAlignment().getHeight() - 1); // BH 2019.04.18 + firePropertyChange("alignment", null, getAlignment().getSequences()); } - /** - * should conservation rows be shown for groups - */ - boolean showGroupConservation = false; + public final static int NO_SPLIT = 0; - /** - * should consensus rows be shown for groups - */ - boolean showGroupConsensus = false; + public final static int SPLIT_FRAME = 1; - /** - * 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 - */ - public boolean showConsensusHistogram = true; + public final static int NEW_WINDOW = 2; /** - * @return the showConsensusProfile + * Show a dialog with the option to open and link (cDNA <-> protein) as a new + * alignment, either as a standalone alignment or in a split frame. Returns + * true if the new alignment was opened, false if not, because the user + * declined the offer. + * + * @param al + * @param title */ - public boolean isShowSequenceLogo() + protected void openLinkedAlignment(AlignmentI al, String title) { - return showSequenceLogo; - } + String[] options = new String[] { MessageManager.getString("action.no"), + MessageManager.getString("label.split_window"), + MessageManager.getString("label.new_window"), }; + final String question = JvSwingUtils.wrapTooltip(true, + MessageManager.getString("label.open_split_window?")); - /** - * @param showSequenceLogo - * the new value + /* + * options No, Split Window, New Window correspond to + * dialog responses 0, 1, 2 (even though JOptionPane shows them + * in reverse order) + */ + JvOptionPane dialog = JvOptionPane + .newOptionDialog(Desktop.getDesktopPane()) + .setResponseHandler(NO_SPLIT, new Runnable() + { + @Override + public void run() + { + addDataToAlignment(al); + } + }).setResponseHandler(SPLIT_FRAME, new Runnable() + { + @Override + public void run() + { + openLinkedAlignmentAs(getAlignPanel().alignFrame, + new Alignment(getAlignment()), al, title, + SPLIT_FRAME); + } + }).setResponseHandler(NEW_WINDOW, new Runnable() + { + @Override + public void run() + { + openLinkedAlignmentAs(null, getAlignment(), al, title, + NEW_WINDOW); + } + }); + dialog.showDialog(question, + MessageManager.getString("label.open_split_window"), + JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null, + options, options[0]); + } + + /** + * Open a split frame or a new window + * + * @param al + * @param title + * @param mode + * SPLIT_FRAME or NEW_WINDOW */ - public void setShowSequenceLogo(boolean showSequenceLogo) + public static void openLinkedAlignmentAs(AlignFrame thisFrame, + AlignmentI thisAlignment, AlignmentI al, String title, int mode) { - if (showSequenceLogo != this.showSequenceLogo) + /* + * Identify protein and dna alignments. Make a copy of this one if opening + * in a new split pane. + */ + AlignmentI protein = al.isNucleotide() ? thisAlignment : al; + AlignmentI cdna = al.isNucleotide() ? al : thisAlignment; + + /* + * Map sequences. At least one should get mapped as we have already passed + * the test for 'mappability'. Any mappings made will be added to the + * protein alignment. Note creating dataset sequences on the new alignment + * is a pre-requisite for building mappings. + */ + al.setDataset(null); + AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna); + + /* + * Create the AlignFrame for the added alignment. If it is protein, mappings + * are registered with StructureSelectionManager as a side-effect. + */ + AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT); + newAlignFrame.setTitle(title); + newAlignFrame.setStatus(MessageManager + .formatMessage("label.successfully_loaded_file", new Object[] + { title })); + + // TODO if we want this (e.g. to enable reload of the alignment from file), + // we will need to add parameters to the stack. + // if (!protocol.equals(DataSourceType.PASTE)) + // { + // alignFrame.setFileName(file, format); + // } + + if (mode == NEW_WINDOW) { - // 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(); - } + Desktop.addInternalFrame(newAlignFrame, title, + AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); + } + + try + { + newAlignFrame.setMaximum(jalview.bin.Cache + .getDefault(Preferences.SHOW_FULLSCREEN, false)); + } catch (java.beans.PropertyVetoException ex) + { + } + + if (mode == SPLIT_FRAME) + { + al.alignAs(thisAlignment); + openSplitFrame(thisFrame, newAlignFrame, thisAlignment); } - this.showSequenceLogo = showSequenceLogo; } /** - * @param showConsensusHistogram - * the showConsensusHistogram to set + * Helper method to open a new SplitFrame holding linked dna and protein + * alignments. + * + * @param newAlignFrame + * containing a new alignment to be shown + * @param complement + * cdna/protein complement alignment to show in the other split half + * @return the protein alignment in the split frame */ - public void setShowConsensusHistogram(boolean showConsensusHistogram) + static protected AlignmentI openSplitFrame(AlignFrame thisFrame, + AlignFrame newAlignFrame, AlignmentI complement) + { + /* + * Make a new frame with a copy of the alignment we are adding to. If this + * is protein, the mappings to cDNA will be registered with + * StructureSelectionManager as a side-effect. + */ + AlignFrame copyMe = new AlignFrame(complement, AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT); + copyMe.setTitle(thisFrame.getTitle()); + + AlignmentI al = newAlignFrame.viewport.getAlignment(); + final AlignFrame proteinFrame = al.isNucleotide() ? copyMe + : newAlignFrame; + final AlignFrame cdnaFrame = al.isNucleotide() ? newAlignFrame : copyMe; + cdnaFrame.setVisible(true); + proteinFrame.setVisible(true); + String linkedTitle = MessageManager + .getString("label.linked_view_title"); + + /* + * Open in split pane. DNA sequence above, protein below. + */ + JInternalFrame splitFrame = new SplitFrame(cdnaFrame, proteinFrame); + Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1); + + return proteinFrame.viewport.getAlignment(); + } + + public AnnotationColumnChooser getAnnotationColumnSelectionState() { - this.showConsensusHistogram = showConsensusHistogram; + return annotationColumnSelectionState; } - /** - * @return the showGroupConservation - */ - public boolean isShowGroupConservation() + public void setAnnotationColumnSelectionState( + AnnotationColumnChooser currentAnnotationColumnSelectionState) { - return showGroupConservation; + this.annotationColumnSelectionState = currentAnnotationColumnSelectionState; } - /** - * @param showGroupConservation - * the showGroupConservation to set - */ - public void setShowGroupConservation(boolean showGroupConservation) + @Override + public void setIdWidth(int i) { - this.showGroupConservation = showGroupConservation; + super.setIdWidth(i); + AlignmentPanel ap = getAlignPanel(); + if (ap != null) + { + // modify GUI elements to reflect geometry change + Dimension idw = getAlignPanel().getIdPanel().getIdCanvas() + .getPreferredSize(); + idw.width = i; + getAlignPanel().getIdPanel().getIdCanvas().setPreferredSize(idw); + } } - /** - * @return the showGroupConsensus - */ - public boolean isShowGroupConsensus() + public Rectangle getExplodedGeometry() { - return showGroupConsensus; + return explodedGeometry; } - /** - * @param showGroupConsensus - * the showGroupConsensus to set - */ - public void setShowGroupConsensus(boolean showGroupConsensus) + public void setExplodedGeometry(Rectangle explodedPosition) { - this.showGroupConsensus = showGroupConsensus; + this.explodedGeometry = explodedPosition; } - /** - * - * @return flag to indicate if the consensus histogram should be rendered by - * default - */ - public boolean isShowConsensusHistogram() + public boolean isGatherViewsHere() + { + return gatherViewsHere; + } + + public void setGatherViewsHere(boolean gatherViewsHere) { - return this.showConsensusHistogram; + this.gatherViewsHere = gatherViewsHere; } /** - * 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. - * - * @param sg - * @param wholewidth + * If this viewport has a (Protein/cDNA) complement, then scroll the + * complementary alignment to match this one. */ - public void expandColSelection(SequenceGroup sg, boolean wholewidth) + public void scrollComplementaryAlignment() { - int sgs, sge; - if (sg != null - && (sgs = sg.getStartRes()) >= 0 - && sg.getStartRes() <= (sge = sg.getEndRes()) - && (colSel == null || colSel.getSelected() == null || colSel - .getSelected().size() == 0)) + /* + * Populate a SearchResults object with the mapped location to scroll to. If + * there is no complement, or it is not following highlights, or no mapping + * is found, the result will be empty. + */ + SearchResultsI sr = new SearchResults(); + int verticalOffset = findComplementScrollTarget(sr); + if (!sr.isEmpty()) { - if (!wholewidth && alignment.getWidth() == (1 + sge - sgs)) - { - // do nothing - return; - } - if (colSel == null) - { - colSel = new ColumnSelection(); - } - for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++) - { - colSel.addElement(cspos); - } + // TODO would like next line without cast but needs more refactoring... + final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement()) + .getAlignPanel(); + complementPanel.setToScrollComplementPanel(false); + complementPanel.scrollToCentre(sr, verticalOffset); + complementPanel.setToScrollComplementPanel(true); } } - public StructureSelectionManager getStructureSelectionManager() - { - return StructureSelectionManager - .getStructureSelectionManager(Desktop.instance); - } - /** + * Answers true if no alignment holds a reference to the given mapping * - * @param pdbEntries - * @return a series of SequenceI arrays, one for each PDBEntry, listing which - * sequence in the alignment holds a reference to it + * @param acf + * @return */ - public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries) + protected boolean noReferencesTo(AlignedCodonFrame acf) { - ArrayList seqvectors = new ArrayList(); - for (PDBEntry pdb : pdbEntries) + AlignFrame[] frames = Desktop.getAlignFrames(); + if (frames == null) { - ArrayList seqs = new ArrayList(); - for (int i = 0; i < alignment.getHeight(); i++) + return true; + } + for (AlignFrame af : frames) + { + if (!af.isClosed()) { - Vector pdbs = alignment.getSequenceAt(i).getDatasetSequence() - .getPDBId(); - if (pdbs == null) - continue; - SequenceI sq; - for (int p = 0; p < pdbs.size(); p++) + for (AlignmentViewPanel ap : af.getAlignPanels()) { - PDBEntry p1 = (PDBEntry) pdbs.elementAt(p); - if (p1.getId().equals(pdb.getId())) + AlignmentI al = ap.getAlignment(); + if (al != null && al.getCodonFrames().contains(acf)) { - if (!seqs.contains(sq = alignment.getSequenceAt(i))) - seqs.add(sq); - - continue; + return false; } } } - 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; - } - - public boolean isCalcInProgress() - { - // TODO generalise to iterate over all calculators associated with av - return updatingConsensus || updatingConservation || updatingStrucConsensus; - } - - public boolean isCalculationInProgress( - AlignmentAnnotation alignmentAnnotation) - { - if (!alignmentAnnotation.autoCalculated) - return false; - if ((updatingConsensus && consensus==alignmentAnnotation) - || (updatingConservation && (conservation==alignmentAnnotation || quality==alignmentAnnotation)) - || (updatingStrucConsensus && strucConsensus==alignmentAnnotation) - ) - { - return true; } - return false; + return true; } /** + * Applies the supplied feature settings descriptor to currently known + * features. This supports an 'initial configuration' of feature colouring + * based on a preset or user favourite. This may then be modified in the usual + * way using the Feature Settings dialogue. * - * @return true if alignment characters should be displayed + * @param featureSettings */ - public boolean isValidCharWidth() - { - return validCharWidth; - } - @Override - public Hashtable[] getSequenceConsensusHash() + public void applyFeaturesStyle(FeatureSettingsModelI featureSettings) { - return hconsensus; - } + if (featureSettings == null) + { + return; + } - @Override - public Hashtable[] getRnaStructureConsensusHash() - { - return hStrucConsensus; - } + FeatureRenderer fr = getAlignPanel().getSeqPanel().seqCanvas + .getFeatureRenderer(); + fr.findAllFeatures(true); + List renderOrder = fr.getRenderOrder(); + FeaturesDisplayedI displayed = fr.getFeaturesDisplayed(); + displayed.clear(); + // TODO this clears displayed.featuresRegistered - do we care? - @Override - public AlignmentAnnotation getAlignmentQualityAnnot() - { - return quality; - } + /* + * set feature colour if specified by feature settings + * set visibility of all features + */ + for (String type : renderOrder) + { + FeatureColourI preferredColour = featureSettings + .getFeatureColour(type); + if (preferredColour != null) + { + fr.setColour(type, preferredColour); + } + if (featureSettings.isFeatureDisplayed(type)) + { + displayed.setVisible(type); + } + } - @Override - public AlignmentAnnotation getAlignmentConservationAnnotation() - { - return conservation; + /* + * set visibility of feature groups + */ + for (String group : fr.getFeatureGroups()) + { + fr.setGroupVisibility(group, featureSettings.isGroupDisplayed(group)); + } + + /* + * order the features + */ + if (featureSettings.optimiseOrder()) + { + // TODO not supported (yet?) + } + else + { + fr.orderFeatures(featureSettings); + } + fr.setTransparency(featureSettings.getTransparency()); } - @Override - public boolean isClosed() + public String getViewName() { - // TODO: check that this isClosed is only true after panel is closed, not before it is fully constructed. - return alignment==null; + return viewName; } - @Override - public AlignCalcManagerI getCalcManager() + public void setViewName(String viewName) { - return calculator; + this.viewName = viewName; } }