X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=a6f7d4130527f93aef06a29c32097849d65ce1a2;hb=6f812eb434553c97cccaaaefa35da54afc72bb79;hp=8c23e4d0121f620ad5e2dd6d62f52827c1f34668;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java old mode 100755 new mode 100644 index 8c23e4d..61b0d1b --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -1,304 +1,248 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) - * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * - * 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. + * This file is part of Jalview. * - * 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 - */ -/* - * 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 + * 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. - * - * 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. - * + * + * 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 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.bin.*; - -import jalview.datamodel.*; - -import jalview.schemes.*; +import jalview.analysis.AlignmentUtils; +import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; +import jalview.api.AlignViewportI; +import jalview.api.AlignmentViewPanel; +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.util.ColorUtils; +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.ArrayList; +import java.util.Hashtable; +import java.util.Iterator; +import java.util.List; + +import javax.swing.JInternalFrame; /** * DOCUMENT ME! * * @author $author$ - * @version $Revision$ + * @version $Revision: 1.141 $ */ -public class AlignViewport implements SelectionSource +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; - // The following vector holds the features which are - // currently visible, in the correct order or rendering - Hashtable featuresDisplayed = null; - - /** DOCUMENT ME!! */ - public Hashtable[] hconsensus; - - AlignmentAnnotation consensus; - - AlignmentAnnotation conservation; - - AlignmentAnnotation quality; - - 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(); - - Stack redoList = new Stack(); - - Hashtable sequenceColours; - - int thresholdTextColour = 0; + private Rectangle explodedGeometry; - Color textColour = Color.black; + private String viewName; - 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. * - * @param al alignment to view + * @param al + * alignment to view */ public AlignViewport(AlignmentI al) { - setAlignment(al); + super(al); init(); } + /** * Create a new AlignViewport object with a specific sequence set ID + * * @param al - * @param seqsetid (may be null - but potential for ambiguous constructor exception) + * @param seqsetid + * (may be null - but potential for ambiguous constructor exception) */ public AlignViewport(AlignmentI al, String seqsetid) { - this(al,seqsetid,null); + this(al, seqsetid, null); } + 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); } - if (Cache.log!=null && Cache.log.isDebugEnabled() && viewId!=null) { Cache.log.debug("Setting viewport's view id : "+viewId); } - setAlignment(al); + if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null) + { + 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); + } init(); + } /** * Create a new AlignViewport with hidden regions * * @param al - * AlignmentI + * AlignmentI * @param hiddenColumns - * ColumnSelection + * 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) - { - hasHiddenColumns = true; - } + al.setHiddenColumns(hiddenColumns); } init(); } + /** * New viewport with hidden columns and an existing sequence set id + * * @param al * @param hiddenColumns - * @param seqsetid (may be null) + * @param seqsetid + * (may be null) */ - public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns, String seqsetid) + public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns, + String seqsetid) { - this(al,hiddenColumns,seqsetid,null); + this(al, hiddenColumns, seqsetid, null); } + /** * New viewport with hidden columns and an existing sequence set id and viewid + * * @param al * @param hiddenColumns - * @param seqsetid (may be null) - * @param viewid (may be null) + * @param seqsetid + * (may be null) + * @param viewid + * (may be null) */ - public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns, String seqsetid, String viewid) + 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); } - if (Cache.log!=null && Cache.log.isDebugEnabled() && viewId!=null) { Cache.log.debug("Setting viewport's view id : "+viewId); } - setAlignment(al); + if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null) + { + 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); + } + if (hiddenColumns != null) { - this.colSel = hiddenColumns; - if (hiddenColumns.getHiddenColumns() != null) - { - hasHiddenColumns = true; - } + 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); - showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true); - showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true); + viewStyle.setShowJVSuffix(Cache.getDefault("SHOW_JVSUFFIX", true)); + setShowAnnotation(Cache.getDefault("SHOW_ANNOTATIONS", true)); - rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false); - centreColumnLabels = Cache.getDefault("CENTRE_COLUMN_LABELS", false); + setRightAlignIds(Cache.getDefault("RIGHT_ALIGN_IDS", false)); + setCentreColumnLabels(Cache.getDefault("CENTRE_COLUMN_LABELS", false)); autoCalculateConsensus = Cache.getDefault("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("PAD_GAPS", true)); + setShowNPFeats(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true)); + setShowDBRefs(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true)); + viewStyle.setSeqNameItalics(Cache.getDefault("ID_ITALICS", true)); + viewStyle.setWrapAlignment(Cache.getDefault("WRAP_ALIGNMENT", false)); + viewStyle.setShowUnconserved( + Cache.getDefault("SHOW_UNCONSERVED", false)); + sortByTree = Cache.getDefault("SORT_BY_TREE", false); + followSelection = Cache.getDefault("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)); + } + + void init() + { + applyViewProperties(); + String fontName = Cache.getDefault("FONT_NAME", "SansSerif"); String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + ""); String fontSize = Cache.getDefault("FONT_SIZE", "10"); - seqNameItalics = Cache.getDefault("ID_ITALICS", true); - int style = 0; if (fontStyle.equals("bold")) @@ -310,7 +254,7 @@ public class AlignViewport 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)); @@ -321,1919 +265,841 @@ public class AlignViewport implements SelectionSource { if (!alignment.isNucleotide()) { - conservation = new AlignmentAnnotation("Conservation", - "Conservation of total alignment less than " + ConsPercGaps - + "% 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); - } + showConservation = Cache.getDefault("SHOW_CONSERVATION", true); + showQuality = Cache.getDefault("SHOW_QUALITY", true); + showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION", + 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; + 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); + showConsensus = Cache.getDefault("SHOW_IDENTITY", true); - if (Cache.getDefault("SHOW_IDENTITY", true)) - { - alignment.addAnnotation(consensus); - } + 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) + { + // 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 (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null) + if (colourScheme instanceof UserColourScheme) { - globalColourScheme = ColourSchemeProperty.getColour(alignment, - jalview.bin.Cache.getProperty("DEFAULT_COLOUR")); + residueShading = new ResidueShader( + UserDefinedColours.loadDefaultColours()); + residueShading.setThreshold(0, isIgnoreGapsConsensus()); + } - if (globalColourScheme instanceof UserColourScheme) - { - globalColourScheme = UserDefinedColours.loadDefaultColours(); - ((UserColourScheme) globalColourScheme).setThreshold(0, - getIgnoreGapsConsensus()); - } + if (residueShading != null) + { + residueShading.setConsensus(hconsensus); + } + setColourAppliesToAllGroups(true); + } - if (globalColourScheme != null) - { - globalColourScheme.setConsensus(hconsensus); - } + boolean validCharWidth; + + /** + * {@inheritDoc} + */ + @Override + public void setFont(Font f, boolean setGrid) + { + font = f; + + Container c = new Container(); + + 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()); - 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); + validCharWidth = true; + } + + @Override + public void setViewStyle(ViewStyleI settingsForView) + { + super.setViewStyle(settingsForView); + setFont(new Font(viewStyle.getFontName(), viewStyle.getFontStyle(), + viewStyle.getFontSize()), false); } /** - * set the flag + * DOCUMENT ME! * - * @param b - * features are displayed if true + * @return DOCUMENT ME! */ - public void setShowSequenceFeatures(boolean b) + public Font getFont() { - showSequenceFeatures = b; + return font; } - public boolean getShowSequenceFeatures() + /** + * DOCUMENT ME! + * + * @param align + * DOCUMENT ME! + */ + @Override + public void setAlignment(AlignmentI align) { - return showSequenceFeatures; + replaceMappings(align); + super.setAlignment(align); } - class ConservationThread extends Thread + /** + * Replace any codon mappings for this viewport with those for the given + * viewport + * + * @param align + */ + public void replaceMappings(AlignmentI align) { - AlignmentPanel ap; - public ConservationThread(AlignmentPanel ap) + /* + * Deregister current mappings (if any) + */ + deregisterMappings(); + + /* + * Register new mappings (if any) + */ + if (align != null) { - this.ap = ap; + StructureSelectionManager ssm = StructureSelectionManager + .getStructureSelectionManager(Desktop.instance); + ssm.registerMappings(align.getCodonFrames()); } - public void run() + /* + * replace mappings on our alignment + */ + if (alignment != null && align != null) { - try - { - updatingConservation = true; - - while (UPDATING_CONSERVATION) - { - try - { - if (ap != null) - { - ap.paintAlignment(false); - } - Thread.sleep(200); - } catch (Exception ex) - { - ex.printStackTrace(); - } - } - - UPDATING_CONSERVATION = true; - - int alWidth = alignment.getWidth(); - if (alWidth < 0) - { - return; - } - - Conservation cons = new jalview.analysis.Conservation("All", - jalview.schemes.ResidueProperties.propHash, 3, alignment - .getSequences(), 0, alWidth - 1); - - cons.calculate(); - cons.verdict(false, ConsPercGaps); - - if (quality != null) - { - cons.findQuality(); - } - - char[] sequence = cons.getConsSequence().getSequence(); - float minR; - float minG; - float minB; - float maxR; - float maxG; - float maxB; - minR = 0.3f; - minG = 0.0f; - minB = 0f; - maxR = 1.0f - minR; - maxG = 0.9f - minG; - maxB = 0f - minB; // scalable range for colouring both Conservation and - // Quality - - float min = 0f; - float max = 11f; - float qmin = 0f; - float qmax = 0f; - - char c; - - conservation.annotations = new Annotation[alWidth]; - - if (quality != null) - { - quality.graphMax = cons.qualityRange[1].floatValue(); - quality.annotations = new Annotation[alWidth]; - qmin = cons.qualityRange[0].floatValue(); - qmax = cons.qualityRange[1].floatValue(); - } + alignment.setCodonFrames(align.getCodonFrames()); + } + } - for (int i = 0; i < alWidth; i++) + protected void deregisterMappings() + { + AlignmentI al = getAlignment(); + if (al != null) + { + List mappings = al.getCodonFrames(); + if (mappings != null) + { + StructureSelectionManager ssm = StructureSelectionManager + .getStructureSelectionManager(Desktop.instance); + for (AlignedCodonFrame acf : mappings) { - float value = 0; - - c = sequence[i]; - - if (Character.isDigit(c)) - { - value = (int) (c - '0'); - } - else if (c == '*') + if (noReferencesTo(acf)) { - value = 11; - } - else if (c == '+') - { - value = 10; - } - - float vprop = value - min; - vprop /= max; - conservation.annotations[i] = new Annotation(String.valueOf(c), - String.valueOf(value), ' ', value, new Color(minR - + (maxR * vprop), minG + (maxG * vprop), minB - + (maxB * vprop))); - - // Quality calc - if (quality != null) - { - value = ((Double) cons.quality.get(i)).floatValue(); - vprop = value - qmin; - vprop /= qmax; - quality.annotations[i] = new Annotation(" ", String - .valueOf(value), ' ', value, new Color(minR - + (maxR * vprop), minG + (maxG * vprop), minB - + (maxB * vprop))); + ssm.deregisterMapping(acf); } } - } catch (OutOfMemoryError error) - { - new OOMWarning("calculating conservation", error); - - conservation = null; - quality = null; - - } - - UPDATING_CONSERVATION = false; - updatingConservation = false; - - if (ap != null) - { - ap.paintAlignment(true); } - } } - 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 + * DOCUMENT ME! + * + * @return DOCUMENT ME! */ - boolean centreColumnLabels = false; - - private boolean showdbrefs; - - private boolean shownpfeats; + @Override + public char getGapCharacter() + { + return getAlignment().getGapCharacter(); + } /** - * trigger update of conservation annotation + * DOCUMENT ME! + * + * @param gap + * DOCUMENT ME! */ - public void updateConservation(final AlignmentPanel ap) + public void setGapCharacter(char gap) { - // see note in mantis : issue number 8585 - if (alignment.isNucleotide() || conservation == null || !autoCalculateConsensus) + if (getAlignment() != null) { - return; + getAlignment().setGapCharacter(gap); } - - conservationThread = new ConservationThread(ap); - conservationThread.start(); } /** - * trigger update of consensus annotation + * returns the visible column regions of the alignment + * + * @param selectedRegionOnly + * true to just return the contigs intersecting with the selected + * area + * @return */ - public void updateConsensus(final AlignmentPanel ap) + public Iterator getViewAsVisibleContigs(boolean selectedRegionOnly) { - // see note in mantis : issue number 8585 - if (consensus == null || !autoCalculateConsensus) + int start = 0; + int end = 0; + if (selectedRegionOnly && selectionGroup != null) { - return; + start = selectionGroup.getStartRes(); + end = selectionGroup.getEndRes() + 1; + } + else + { + end = alignment.getWidth(); } - consensusThread = new ConsensusThread(ap); - consensusThread.start(); + return (alignment.getHiddenColumns().getVisContigsIterator(start, end, + false)); } - class ConsensusThread extends Thread + /** + * get hash of undo and redo list for the alignment + * + * @return long[] { historyList.hashCode, redoList.hashCode }; + */ + public long[] getUndoRedoHash() { - AlignmentPanel ap; + // TODO: JAL-1126 + if (historyList == null || redoList == null) + { + return new long[] { -1, -1 }; + } + return new long[] { historyList.hashCode(), this.redoList.hashCode() }; + } - public ConsensusThread(AlignmentPanel ap) + /** + * 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) { - this.ap = ap; + return true; } - public void run() + for (int i = 0; i < cstate.length; i++) { - updatingConsensus = true; - while (UPDATING_CONSENSUS) + if (cstate[i] != undoredo[i]) { - 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() : 0; // null - // pointer - // possibility - // here. - if (aWidth < 0) - { - return; - } - - consensus.annotations = null; - consensus.annotations = new Annotation[aWidth]; - - hconsensus = new Hashtable[aWidth]; - AAFrequency.calculate(alignment.getSequencesArray(), 0, alignment - .getWidth(), hconsensus); - - for (int i = 0; i < aWidth; i++) - { - float value = 0; - if (ignoreGapsInConsensusCalculation) - { - value = ((Float) hconsensus[i].get(AAFrequency.PID_NOGAPS)) - .floatValue(); - } - else - { - value = ((Float) hconsensus[i].get(AAFrequency.PID_GAPS)) - .floatValue(); - } - - String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE) - .toString(); - String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) - + " "; - - if (maxRes.length() > 1) - { - mouseOver = "[" + maxRes + "] "; - maxRes = "+"; - } - - mouseOver += ((int) value + "%"); - consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ', - value); - } - - 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); + return true; } } + return false; } - /** - * 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; - } + public boolean followSelection = true; /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! + * @return true if view selection should always follow the selections + * broadcast by other selection sources */ - public SequenceGroup getSelectionGroup() + public boolean getFollowSelection() { - return selectionGroup; + return followSelection; } /** - * DOCUMENT ME! - * - * @param sg - * DOCUMENT ME! + * Send the current selection to be broadcast to any selection listeners. */ - public void setSelectionGroup(SequenceGroup sg) + @Override + public void sendSelection() { - selectionGroup = sg; + jalview.structure.StructureSelectionManager + .getStructureSelectionManager(Desktop.instance) + .sendSelection(new SequenceGroup(getSelectionGroup()), + new ColumnSelection(getColumnSelection()), + new HiddenColumns(getAlignment().getHiddenColumns()), + this); } /** - * DOCUMENT ME! + * return the alignPanel containing the given viewport. Use this to get the + * components currently handling the given viewport. * - * @return DOCUMENT ME! + * @param av + * @return null or an alignPanel guaranteed to have non-null alignFrame + * reference */ - public boolean getConservationSelected() + public AlignmentPanel getAlignPanel() { - return conservationColourSelected; + 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; } - /** - * DOCUMENT ME! - * - * @param b - * DOCUMENT ME! - */ - public void setConservationSelected(boolean b) + public boolean getSortByTree() { - conservationColourSelected = b; + return sortByTree; } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getAbovePIDThreshold() + public void setSortByTree(boolean sort) { - return abovePIDThreshold; + sortByTree = sort; } /** - * DOCUMENT ME! - * - * @param b - * DOCUMENT ME! + * Returns the (Desktop) instance of the StructureSelectionManager */ - public void setAbovePIDThreshold(boolean b) + @Override + public StructureSelectionManager getStructureSelectionManager() { - abovePIDThreshold = b; + return StructureSelectionManager + .getStructureSelectionManager(Desktop.instance); } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getStartRes() + @Override + public boolean isNormaliseSequenceLogo() { - return startRes; + return normaliseSequenceLogo; } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getEndRes() + public void setNormaliseSequenceLogo(boolean state) { - return endRes; + normaliseSequenceLogo = state; } /** - * DOCUMENT ME! * - * @return DOCUMENT ME! + * @return true if alignment characters should be displayed */ - public int getStartSeq() + @Override + public boolean isValidCharWidth() { - return startSeq; + return validCharWidth; } - /** - * DOCUMENT ME! - * - * @param cs - * DOCUMENT ME! - */ - public void setGlobalColourScheme(ColourSchemeI cs) - { - globalColourScheme = cs; - } + private Hashtable calcIdParams = new Hashtable<>(); - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public ColourSchemeI getGlobalColourScheme() + public AutoCalcSetting getCalcIdSettingsFor(String calcId) { - return globalColourScheme; + return calcIdParams.get(calcId); } - /** - * DOCUMENT ME! - * - * @param res - * DOCUMENT ME! - */ - public void setStartRes(int res) + public void setCalcIdSettingsFor(String calcId, AutoCalcSetting settings, + boolean needsUpdate) { - this.startRes = res; + 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) + { + Cache.log.debug("trigger update for " + calcId); + } } /** - * DOCUMENT ME! + * 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 seq - * DOCUMENT ME! + * @param command + * @param undo + * @param ssm */ - public void setStartSeq(int seq) + @Override + public void mirrorCommand(CommandI command, boolean undo, + StructureSelectionManager ssm, VamsasSource source) { - this.startSeq = seq; + /* + * 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) + { + // ok to continue; + } + else + { + return; + } + + CommandI mappedCommand = ssm.mapCommand(command, undo, getAlignment(), + getGapCharacter()); + if (mappedCommand != null) + { + AlignmentI[] views = getAlignPanel().alignFrame.getViewAlignments(); + mappedCommand.doCommand(views); + getAlignPanel().alignmentChanged(); + } } /** - * DOCUMENT ME! + * 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 res - * DOCUMENT ME! + * @param toAdd + * @param title */ - public void setEndRes(int res) + public void addAlignment(AlignmentI toAdd, String title) { - if (res > (alignment.getWidth() - 1)) + // TODO: promote to AlignViewportI? applet CutAndPasteTransfer is different + + // 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 + + // refactored from FileLoader / CutAndPasteTransfer / SequenceFetcher with + // this comment: + // TODO: create undo object for this JAL-1101 + + /* + * Ensure datasets are created for the new alignment as + * mappings operate on dataset sequences + */ + toAdd.setDataset(null); + + /* + * 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)) { - // log.System.out.println(" Corrected res from " + res + " to maximum " + - // (alignment.getWidth()-1)); - res = alignment.getWidth() - 1; + if (AlignmentUtils.isMappable(toAdd, getAlignment())) + { + if (openLinkedAlignment(toAdd, title)) + { + return; + } + } } - if (res < 0) - { - res = 0; + /* + * No mappings, or offer declined - add sequences to this alignment + */ + // 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++) + { + 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)*/) + { + al.addSequence(seq); + } } - this.endRes = res; + ranges.setEndSeq(getAlignment().getHeight()); + firePropertyChange("alignment", null, getAlignment().getSequences()); } /** - * DOCUMENT ME! + * 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 seq - * DOCUMENT ME! + * @param al + * @param title */ - public void setEndSeq(int seq) + protected boolean openLinkedAlignment(AlignmentI al, String title) { - if (seq > alignment.getHeight()) + 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?")); + int response = JvOptionPane.showOptionDialog(Desktop.desktop, question, + MessageManager.getString("label.open_split_window"), + JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null, + options, options[0]); + + if (response != 1 && response != 2) + { + return false; + } + final boolean openSplitPane = (response == 1); + final boolean openInNewWindow = (response == 2); + + /* + * Identify protein and dna alignments. Make a copy of this one if opening + * in a new split pane. + */ + AlignmentI thisAlignment = openSplitPane ? new Alignment(getAlignment()) + : getAlignment(); + AlignmentI protein = al.isNucleotide() ? thisAlignment : al; + final 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 (openInNewWindow) { - seq = alignment.getHeight(); + Desktop.addInternalFrame(newAlignFrame, title, + AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); } - if (seq < 0) + try + { + newAlignFrame.setMaximum( + jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false)); + } catch (java.beans.PropertyVetoException ex) { - seq = 0; } - this.endSeq = seq; - } + if (openSplitPane) + { + al.alignAs(thisAlignment); + protein = openSplitFrame(newAlignFrame, thisAlignment); + } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getEndSeq() - { - return endSeq; + return true; } /** - * DOCUMENT ME! + * Helper method to open a new SplitFrame holding linked dna and protein + * alignments. * - * @param f - * DOCUMENT ME! + * @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 setFont(Font f) + protected AlignmentI openSplitFrame(AlignFrame newAlignFrame, + AlignmentI complement) { - font = f; + /* + * 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(getAlignPanel().alignFrame.getTitle()); - Container c = new Container(); + 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"); - java.awt.FontMetrics fm = c.getFontMetrics(font); - setCharHeight(fm.getHeight()); - setCharWidth(fm.charWidth('M')); - validCharWidth = true; + /* + * 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(); } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public Font getFont() + public AnnotationColumnChooser getAnnotationColumnSelectionState() { - return font; + return annotationColumnSelectionState; } - /** - * DOCUMENT ME! - * - * @param w - * DOCUMENT ME! - */ - public void setCharWidth(int w) + public void setAnnotationColumnSelectionState( + AnnotationColumnChooser currentAnnotationColumnSelectionState) { - this.charWidth = w; + this.annotationColumnSelectionState = currentAnnotationColumnSelectionState; } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getCharWidth() + @Override + public void setIdWidth(int i) { - return charWidth; + 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); + } } - /** - * DOCUMENT ME! - * - * @param h - * DOCUMENT ME! - */ - public void setCharHeight(int h) + public Rectangle getExplodedGeometry() { - this.charHeight = h; + return explodedGeometry; } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getCharHeight() + public void setExplodedGeometry(Rectangle explodedPosition) { - return charHeight; + this.explodedGeometry = explodedPosition; } - /** - * DOCUMENT ME! - * - * @param w - * DOCUMENT ME! - */ - public void setWrappedWidth(int w) + public boolean isGatherViewsHere() { - this.wrappedWidth = w; + return gatherViewsHere; } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getWrappedWidth() + public void setGatherViewsHere(boolean gatherViewsHere) { - return wrappedWidth; + this.gatherViewsHere = gatherViewsHere; } /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! + * If this viewport has a (Protein/cDNA) complement, then scroll the + * complementary alignment to match this one. */ - public AlignmentI getAlignment() + public void scrollComplementaryAlignment() { - return alignment; + /* + * 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()) + { + // 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); + } } /** - * DOCUMENT ME! + * Answers true if no alignment holds a reference to the given mapping * - * @param align - * DOCUMENT ME! + * @param acf + * @return */ - public void setAlignment(AlignmentI align) + protected boolean noReferencesTo(AlignedCodonFrame acf) { - if (alignment != null && alignment.getCodonFrames() != null) + AlignFrame[] frames = Desktop.getAlignFrames(); + if (frames == null) { - StructureSelectionManager.getStructureSelectionManager() - .removeMappings(alignment.getCodonFrames()); + return true; } - this.alignment = align; - if (alignment.getCodonFrames() != null) + for (AlignFrame af : frames) { - StructureSelectionManager.getStructureSelectionManager().addMappings( - alignment.getCodonFrames()); + if (!af.isClosed()) + { + for (AlignmentViewPanel ap : af.getAlignPanels()) + { + AlignmentI al = ap.getAlignment(); + if (al != null && al.getCodonFrames().contains(acf)) + { + return false; + } + } + } } + return true; } /** - * DOCUMENT ME! + * 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. * - * @param state - * DOCUMENT ME! + * @param featureSettings */ - public void setWrapAlignment(boolean state) + @Override + public void applyFeaturesStyle(FeatureSettingsModelI featureSettings) { - wrapAlignment = state; + transferFeaturesStyles(featureSettings, false); } /** - * DOCUMENT ME! + * 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. * - * @param state - * DOCUMENT ME! + * @param featureSettings */ - public void setShowText(boolean state) + @Override + public void mergeFeaturesStyle(FeatureSettingsModelI featureSettings) { - showText = state; + transferFeaturesStyles(featureSettings, true); } /** - * DOCUMENT ME! + * when mergeOnly is set, then group and feature visibility or feature colours + * are not modified for features and groups already known to the feature + * renderer. Feature ordering is always adjusted, and transparency is always set + * regardless. * - * @param state - * DOCUMENT ME! + * @param featureSettings + * @param mergeOnly */ - public void setRenderGaps(boolean state) + private void transferFeaturesStyles(FeatureSettingsModelI featureSettings, + boolean mergeOnly) { - renderGaps = state; - } + if (featureSettings == null) + { + return; + } + + FeatureRenderer fr = getAlignPanel().getSeqPanel().seqCanvas + .getFeatureRenderer(); + List origRenderOrder = new ArrayList(), + origGroups = new ArrayList(); + // preserve original render order - allows differentiation between user configured colours and autogenerated ones + origRenderOrder.addAll(fr.getRenderOrder()); + origGroups.addAll(fr.getFeatureGroups()); + + fr.findAllFeatures(true); + List renderOrder = fr.getRenderOrder(); + FeaturesDisplayedI displayed = fr.getFeaturesDisplayed(); + if (!mergeOnly) + { + // only clear displayed features if we are mergeing + displayed.clear(); + } + // TODO this clears displayed.featuresRegistered - do we care? + // + // JAL-3330 - JBP - yes we do - calling applyFeatureStyle to a view where + // feature visibility has already been configured is not very friendly + /* + * set feature colour if specified by feature settings + * set visibility of all features + */ + for (String type : renderOrder) + { + FeatureColourI preferredColour = featureSettings + .getFeatureColour(type); + FeatureColourI origColour = fr.getFeatureStyle(type); + if (!mergeOnly || (!origRenderOrder.contains(type) + || origColour == null + || (!origColour.isGraduatedColour() + && origColour.getColour() != null + && origColour.getColour().equals( + ColorUtils.createColourFromName(type))))) + { + // if we are merging, only update if there wasn't already a colour defined for + // this type + if (preferredColour != null) + { + fr.setColour(type, preferredColour); + } + if (featureSettings.isFeatureDisplayed(type)) + { + displayed.setVisible(type); + } + } + } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getColourText() - { - return showColourText; + /* + * set visibility of feature groups + */ + for (String group : fr.getFeatureGroups()) + { + if (!mergeOnly || !origGroups.contains(group)) + { + // when merging, display groups only if the aren't already marked as not visible + fr.setGroupVisibility(group, + featureSettings.isGroupDisplayed(group)); + } + } + + /* + * order the features + */ + if (featureSettings.optimiseOrder()) + { + // TODO not supported (yet?) + } + else + { + fr.orderFeatures(featureSettings); + } + fr.setTransparency(featureSettings.getTransparency()); } - /** - * DOCUMENT ME! - * - * @param state - * DOCUMENT ME! - */ - public void setColourText(boolean state) + public String getViewName() { - showColourText = state; + return viewName; } - /** - * 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) - { - CigarArray selection = null; - SequenceI[] seqs = null; - int i, iSize; - int start = 0, end = 0; - if (selectedRegionOnly && selectionGroup != null) - { - iSize = selectionGroup.getSize(); - seqs = selectionGroup.getSequencesInOrder(alignment); - start = selectionGroup.getStartRes(); - end = selectionGroup.getEndRes(); // inclusive for start and end in - // SeqCigar constructor - } - else - { - iSize = alignment.getHeight(); - seqs = alignment.getSequencesArray(); - end = alignment.getWidth() - 1; - } - SeqCigar[] selseqs = new SeqCigar[iSize]; - for (i = 0; i < iSize; i++) - { - selseqs[i] = new SeqCigar(seqs[i], start, end); - } - selection = new CigarArray(selseqs); - // now construct the CigarArray operations - if (hasHiddenColumns) - { - Vector regions = colSel.getHiddenColumns(); - int[] region; - int hideStart, hideEnd; - int last = start; - for (int j = 0; last < end & j < regions.size(); j++) - { - region = (int[]) regions.elementAt(j); - hideStart = region[0]; - hideEnd = region[1]; - // edit hidden regions to selection range - if (hideStart < last) - { - if (hideEnd > last) - { - hideStart = last; - } - else - { - continue; - } - } - - if (hideStart > end) - { - break; - } - - if (hideEnd > end) - { - hideEnd = end; - } - - if (hideStart > hideEnd) - { - break; - } - /** - * form operations... - */ - if (last < hideStart) - { - selection.addOperation(CigarArray.M, hideStart - last); - } - selection.addOperation(CigarArray.D, 1 + hideEnd - hideStart); - last = hideEnd + 1; - } - // Final match if necessary. - if (last < end) - { - selection.addOperation(CigarArray.M, end - last + 1); - } - } - else - { - selection.addOperation(CigarArray.M, end - start + 1); - } - return selection; - } - - /** - * return a compact representation of the current alignment selection to pass - * to an analysis function - * - * @param selectedOnly - * boolean true to just return the selected view - * @return AlignmentView - */ - jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly) - { - // JBPNote: - // this is here because the AlignmentView constructor modifies the - // CigarArray - // object. Refactoring of Cigar and alignment view representation should - // be done to remove redundancy. - CigarArray aligview = getViewAsCigars(selectedOnly); - if (aligview != null) - { - return new AlignmentView(aligview, - (selectedOnly && selectionGroup != null) ? selectionGroup - .getStartRes() : 0); - } - return null; - } - - /** - * 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); - } - - // 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)) - { - 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); - } - } - } - } - - /** - * enable or disable the display of Database Cross References in the sequence ID tooltip - */ - public void setShowDbRefs(boolean show) - { - showdbrefs=show; - } - - /** - * - * @return true if Database References are to be displayed on tooltips. - */ - public boolean isShowDbRefs() - { - return showdbrefs; - } - - /** - * - * @return true if Non-positional features are to be displayed on tooltips. - */ - public boolean isShowNpFeats() - { - return shownpfeats; - } - /** - * enable or disable the display of Non-Positional sequence features in the sequence ID tooltip - * @param show - */ - public void setShowNpFeats(boolean show) - { - shownpfeats=show; - } - /** - * - * @return true if view has hidden rows - */ - public boolean hasHiddenRows() - { - return hasHiddenRows; - } - /** - * - * @return true if view has hidden columns - */ - public boolean hasHiddenColumns() - { - return hasHiddenColumns; - } - /** - * 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() { - return followHighlight; - } - public boolean followSelection=true; - /** - * @return true if view selection should always follow the selections broadcast by other selection sources - */ - public boolean getFollowSelection() { - 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(new SequenceGroup(getSelectionGroup()), new ColumnSelection(getColumnSelection()), this); - } - public void setShowSequenceFeaturesHeight(boolean selected) - { - showSeqFeaturesHeight = selected; - } - public boolean getShowSequenceFeaturesHeight() - { - 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. - * @param av - * @return null or an alignPanel guaranteed to have non-null alignFrame reference - */ - public AlignmentPanel getAlignPanel() - { - AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(this.getSequenceSetId()); - AlignmentPanel ap=null; - for (int p=0;aps!=null && p