X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=fd1fa7d992089a066fec858fff415cce7c7f5747;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=84cbe76b6e982aa2d22a6060921f633dd538469b;hpb=b6d133ff2200a05764410900ed01b75760860fcf;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java old mode 100755 new mode 100644 index 84cbe76..8a95015 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -1,6 +1,26 @@ - /* +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 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. + * + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +/* * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * 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 @@ -18,1398 +38,1073 @@ */ package jalview.gui; -import jalview.analysis.*; - -import jalview.bin.*; - -import jalview.datamodel.*; - -import jalview.schemes.*; - -import java.awt.*; - -import java.util.*; - +import jalview.analysis.AlignmentUtils; +import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; +import jalview.analysis.NJTree; +import jalview.api.AlignViewportI; +import jalview.api.AlignmentViewPanel; +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.PDBEntry; +import jalview.datamodel.SearchResults; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.schemes.ColourSchemeProperty; +import jalview.schemes.UserColourScheme; +import jalview.structure.CommandListener; +import jalview.structure.SelectionSource; +import jalview.structure.StructureSelectionManager; +import jalview.structure.VamsasSource; +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.Rectangle; +import java.util.ArrayList; +import java.util.Hashtable; +import java.util.List; +import java.util.Set; +import java.util.Vector; + +import javax.swing.JInternalFrame; +import javax.swing.JOptionPane; /** * DOCUMENT ME! - * + * * @author $author$ - * @version $Revision$ + * @version $Revision: 1.141 $ */ -public class AlignViewport +public class AlignViewport extends AlignmentViewport implements + SelectionSource, CommandListener { - 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 showConservation = true; - boolean showQuality = true; - boolean showIdentity = 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; - 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; - - - public AlignViewport(AlignmentI al, boolean dataset) - { - isDataset = dataset; - setAlignment(al); - init(); + Font font; + + NJTree currentTree = null; + + boolean cursorMode = false; + + boolean antiAlias = false; + + private Rectangle explodedGeometry; + + String viewName; + + /* + * 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; + + private AnnotationColumnChooser annotationColumnSelectionState; + + /** + * Creates a new AlignViewport object. + * + * @param al + * alignment to view + */ + public AlignViewport(AlignmentI al) + { + setAlignment(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) + */ + public AlignViewport(AlignmentI al, String seqsetid) + { + this(al, seqsetid, null); + } + + public AlignViewport(AlignmentI al, String seqsetid, String viewid) + { + 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); + init(); + } + + /** + * Create a new AlignViewport with hidden regions + * + * @param al + * AlignmentI + * @param hiddenColumns + * ColumnSelection + */ + public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns) + { + setAlignment(al); + if (hiddenColumns != null) + { + colSel = hiddenColumns; + } + init(); + } + + /** + * New viewport with hidden columns and an existing sequence set id + * + * @param al + * @param hiddenColumns + * @param seqsetid + * (may be null) + */ + public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns, + String seqsetid) + { + 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) + */ + public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns, + String seqsetid, String viewid) + { + 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 (hiddenColumns != null) + { + colSel = hiddenColumns; + } + init(); + } + + /** + * Apply any settings saved in user preferences + */ + private void applyViewProperties() + { + antiAlias = Cache.getDefault("ANTI_ALIAS", false); + + viewStyle.setShowJVSuffix(Cache.getDefault("SHOW_JVSUFFIX", true)); + setShowAnnotation(Cache.getDefault("SHOW_ANNOTATIONS", true)); + + setRightAlignIds(Cache.getDefault("RIGHT_ALIGN_IDS", false)); + setCentreColumnLabels(Cache.getDefault("CENTRE_COLUMN_LABELS", false)); + autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", 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() + { + this.startRes = 0; + this.endRes = alignment.getWidth() - 1; + this.startSeq = 0; + this.endSeq = alignment.getHeight() - 1; + applyViewProperties(); + + String fontName = Cache.getDefault("FONT_NAME", "SansSerif"); + String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + ""); + String fontSize = Cache.getDefault("FONT_SIZE", "10"); + + int style = 0; + + if (fontStyle.equals("bold")) + { + style = 1; + } + else if (fontStyle.equals("italic")) + { + style = 2; + } + + setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true); + + alignment + .setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0)); + + // We must set conservation and consensus before setting colour, + // as Blosum and Clustal require this to be done + if (hconsensus == null && !isDataset) + { + if (!alignment.isNucleotide()) + { + showConservation = Cache.getDefault("SHOW_CONSERVATION", true); + showQuality = Cache.getDefault("SHOW_QUALITY", true); + 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); + showConsensus = Cache.getDefault("SHOW_IDENTITY", true); } - /** - * Creates a new AlignViewport object. - * - * @param al DOCUMENT ME! - */ - public AlignViewport(AlignmentI al) + initAutoAnnotation(); + String colourProperty = alignment.isNucleotide() ? Preferences.DEFAULT_COLOUR_NUC + : Preferences.DEFAULT_COLOUR_PROT; + String propertyValue = Cache.getProperty(colourProperty); + if (propertyValue == null) { - setAlignment(al); - init(); - } - /** - * Create a new AlignViewport with hidden regions - * @param al AlignmentI - * @param hiddenColumns ColumnSelection - */ - public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns) { - setAlignment(al); - if (hiddenColumns!=null) { - this.colSel = hiddenColumns; - if (hiddenColumns.getHiddenColumns() != null) - hasHiddenColumns = true; - } - init(); + // fall back on this property for backwards compatibility + propertyValue = Cache.getProperty(Preferences.DEFAULT_COLOUR); } - - void init() + if (propertyValue != null) { - 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); - showConservation = Cache.getDefault("SHOW_CONSERVATION", true); - - showQuality = Cache.getDefault("SHOW_QUALITY", true); - showIdentity = Cache.getDefault("SHOW_IDENTITY", true); - - autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true); - - padGaps = Cache.getDefault("PAD_GAPS", false); - - String fontName = Cache.getDefault("FONT_NAME", "SansSerif"); - String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ; - String fontSize = Cache.getDefault("FONT_SIZE", "10"); - - int style = 0; - - if (fontStyle.equals("bold")) - { - style = 1; - } - else if (fontStyle.equals("italic")) - { - style = 2; - } - - setFont(new Font(fontName, style, Integer.parseInt(fontSize))); - - - alignment.setGapCharacter( Cache.getDefault("GAP_SYMBOL", "-").charAt(0) ); - + globalColourScheme = ColourSchemeProperty.getColour(alignment, + propertyValue); - // We must set conservation and consensus before setting colour, - // as Blosum and Clustal require this to be done - if(hconsensus==null && !isDataset) - { - updateConservation(); - updateConsensus(); - } - - if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null) - { - globalColourScheme = ColourSchemeProperty.getColour(alignment, - jalview.bin.Cache.getProperty("DEFAULT_COLOUR")); - - if (globalColourScheme instanceof UserColourScheme) - { - globalColourScheme = UserDefinedColours.loadDefaultColours(); - ((UserColourScheme)globalColourScheme).setThreshold(0, getIgnoreGapsConsensus()); - } + if (globalColourScheme instanceof UserColourScheme) + { + globalColourScheme = UserDefinedColours.loadDefaultColours(); + ((UserColourScheme) globalColourScheme).setThreshold(0, + isIgnoreGapsConsensus()); + } - if (globalColourScheme != null) - { - globalColourScheme.setConsensus(hconsensus); - } - } + if (globalColourScheme != null) + { + globalColourScheme.setConsensus(hconsensus); + } } + } - - - /** - * DOCUMENT ME! - * - * @param b DOCUMENT ME! - */ - public void setShowSequenceFeatures(boolean b) + /** + * 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) { - showSequenceFeatures = b; + updateConsensus(null); } - - public boolean getShowSequenceFeatures() + if (consensus == null) { - return showSequenceFeatures; + return null; } - - /** - * DOCUMENT ME! - */ - public void updateConservation() + StringBuffer seqs = new StringBuffer(); + for (int i = 0; i < consensus.annotations.length; i++) { - if(alignment.isNucleotide()) - return; - - // System.out.println("UPDATING CONSERVATION"); - - try{ - Conservation cons = new jalview.analysis.Conservation("All", - jalview.schemes.ResidueProperties.propHash, 3, - alignment.getSequences(), 0, alignment.getWidth() - 1); - cons.calculate(); - cons.verdict(false, ConsPercGaps); - cons.findQuality(); - - int alWidth = alignment.getWidth(); - Annotation[] annotations = new Annotation[alWidth]; - Annotation[] qannotations = new Annotation[alWidth]; - String 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 = cons.qualityRange[0].floatValue(); - float qmax = cons.qualityRange[1].floatValue(); - - for (int i = 0; i < alWidth; i++) - { - float value = 0; - - try - { - value = Integer.parseInt(sequence.charAt(i) + ""); - } - catch (Exception ex) - { - if (sequence.charAt(i) == '*') - { - value = 11; - } - - if (sequence.charAt(i) == '+') - { - value = 10; - } - } - - float vprop = value - min; - vprop /= max; - annotations[i] = new Annotation(sequence.charAt(i) + "", - String.valueOf(value), ' ', value, - new Color(minR + (maxR * vprop), - minG + (maxG * vprop), - minB + (maxB * vprop))); - - // Quality calc - value = ( (Double) cons.quality.get(i)).floatValue(); - vprop = value - qmin; - vprop /= qmax; - qannotations[i] = new Annotation(" ", String.valueOf(value), ' ', - value, - new Color(minR + (maxR * vprop), - minG + (maxG * vprop), - minB + (maxB * vprop))); - } - - if (conservation == null) + if (consensus.annotations[i] != null) + { + if (consensus.annotations[i].description.charAt(0) == '[') { - conservation = new AlignmentAnnotation("Conservation", - "Conservation of total alignment less than " + - ConsPercGaps + "% gaps", - annotations, 0f, // cons.qualityRange[0].floatValue(), - 11f, // cons.qualityRange[1].floatValue() - AlignmentAnnotation.BAR_GRAPH); - - if (showConservation) - { - alignment.addAnnotation(conservation); - } - - quality = new AlignmentAnnotation("Quality", - "Alignment Quality based on Blosum62 scores", - qannotations, - cons.qualityRange[0].floatValue(), - cons.qualityRange[1].floatValue(), - AlignmentAnnotation.BAR_GRAPH); - - if (showQuality) - { - alignment.addAnnotation(quality); - } + seqs.append(consensus.annotations[i].description.charAt(1)); } else { - conservation.annotations = annotations; - quality.annotations = qannotations; - quality.graphMax = cons.qualityRange[1].floatValue(); + seqs.append(consensus.annotations[i].displayCharacter); } } - catch (OutOfMemoryError error) - { - javax.swing.SwingUtilities.invokeLater(new Runnable() - { - public void run() - { - javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop, - "Out of memory calculating conservation!!" - + - "\nSee help files for increasing Java Virtual Machine memory." - , "Out of memory", - javax.swing.JOptionPane.WARNING_MESSAGE); - } - }); - - System.out.println("Conservation calculation: " + error); - System.gc(); - - } } - - /** - * DOCUMENT ME! - */ - public void updateConsensus() - { - try{ - int aWidth = alignment.getWidth(); - - Annotation[] 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("pid_nogaps")).floatValue(); - else - value = ( (Float) hconsensus[i].get("pid_gaps")).floatValue(); - - String maxRes = hconsensus[i].get("maxResidue").toString(); - String mouseOver = hconsensus[i].get("maxResidue") + " "; - - if (maxRes.length() > 1) - { - mouseOver = "[" + maxRes + "] "; - maxRes = "+"; - } - - mouseOver += ( (int) value + "%"); - annotations[i] = new Annotation(maxRes, mouseOver, ' ', value); - } - - if (consensus == null) - { - consensus = new AlignmentAnnotation("Consensus", "PID", - annotations, 0f, 100f,AlignmentAnnotation.BAR_GRAPH); - - if (showIdentity) - { - alignment.addAnnotation(consensus); - } - } - else - { - consensus.annotations = annotations; - } - - if (globalColourScheme != null) - globalColourScheme.setConsensus(hconsensus); - - }catch(OutOfMemoryError error) + SequenceI sq = new Sequence("Consensus", seqs.toString()); + sq.setDescription("Percentage Identity Consensus " + + ((ignoreGapsInConsensusCalculation) ? " without gaps" : "")); + return sq; + } + + boolean validCharWidth; + + /** + * update view settings with the given font. You may need to call + * alignPanel.fontChanged to update the layout geometry + * + * @param setGrid + * when true, charWidth/height is set according to font mentrics + */ + public void setFont(Font f, boolean setGrid) + { + font = f; + + Container c = new Container(); + + java.awt.FontMetrics fm = c.getFontMetrics(font); + int w = viewStyle.getCharWidth(), ww = fm.charWidth('M'), h = viewStyle + .getCharHeight(); + if (setGrid) + { + setCharHeight(fm.getHeight()); + setCharWidth(ww); + } + viewStyle.setFontName(font.getName()); + viewStyle.setFontStyle(font.getStyle()); + viewStyle.setFontSize(font.getSize()); + + validCharWidth = true; + } + + @Override + public void setViewStyle(ViewStyleI settingsForView) + { + super.setViewStyle(settingsForView); + setFont(new Font(viewStyle.getFontName(), viewStyle.getFontStyle(), + viewStyle.getFontSize()), false); + + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public Font getFont() + { + return font; + } + + /** + * DOCUMENT ME! + * + * @param align + * DOCUMENT ME! + */ + public void setAlignment(AlignmentI align) + { + replaceMappings(align); + this.alignment = align; + } + + /** + * Replace any codon mappings for this viewport with those for the given + * viewport + * + * @param align + */ + public void replaceMappings(AlignmentI align) + { + + /* + * Deregister current mappings (if any) + */ + deregisterMappings(); + + /* + * Register new mappings (if any) + */ + if (align != null) + { + StructureSelectionManager ssm = StructureSelectionManager + .getStructureSelectionManager(Desktop.instance); + ssm.registerMappings(align.getCodonFrames()); + } + + /* + * replace mappings on our alignment + */ + if (alignment != null && align != null) + { + alignment.setCodonFrames(align.getCodonFrames()); + } + } + + protected void deregisterMappings() + { + AlignmentI al = getAlignment(); + if (al != null) + { + Set mappings = al.getCodonFrames(); + if (mappings != null) { - javax.swing.SwingUtilities.invokeLater(new Runnable() + StructureSelectionManager ssm = StructureSelectionManager + .getStructureSelectionManager(Desktop.instance); + for (AlignedCodonFrame acf : mappings) { - public void run() + if (noReferencesTo(acf)) { - javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop, - "Out of memory calculating consensus!!" - + - "\nSee help files for increasing Java Virtual Machine memory." - , "Out of memory", - javax.swing.JOptionPane.WARNING_MESSAGE); + ssm.deregisterMapping(acf); } - }); - - - System.out.println("Consensus calculation: " + error); - System.gc(); - } - - } - /** - * 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(); - if (consensus==null) - return null; - StringBuffer seqs=new StringBuffer(); - for (int i=0; i (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) - { - this.alignment = align; - } - - /** - * 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) - { - ignoreGapsInConsensusCalculation = b; - updateConsensus(); - if(globalColourScheme!=null) + } + + /** + * 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! + * + * @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; + } + + /** + * 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() + { + // TODO: JAL-1126 + 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]) { - globalColourScheme.setThreshold(globalColourScheme.getThreshold(), ignoreGapsInConsensusCalculation); + return true; } } - - 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; + return false; + } + + public boolean followSelection = true; + + /** + * @return true if view selection should always follow the selections + * broadcast by other selection sources + */ + public boolean getFollowSelection() + { + return followSelection; + } + + /** + * Send the current selection to be broadcast to any selection listeners. + */ + public void sendSelection() + { + jalview.structure.StructureSelectionManager + .getStructureSelectionManager(Desktop.instance).sendSelection( + new SequenceGroup(getSelectionGroup()), + new ColumnSelection(getColumnSelection()), this); + } + + /** + * 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()); + for (int p = 0; aps != null && p < aps.length; p++) + { + if (aps[p].av == this) + { + return aps[p]; + } } - - public void hideAllSelectedSeqs() - { - if (selectionGroup == null) + return null; + } + + public boolean getSortByTree() + { + return sortByTree; + } + + public void setSortByTree(boolean sort) + { + sortByTree = sort; + } + + /** + * 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 + */ + public void expandColSelection(SequenceGroup sg, boolean wholewidth) + { + int sgs, sge; + if (sg != null + && (sgs = sg.getStartRes()) >= 0 + && sg.getStartRes() <= (sge = sg.getEndRes()) + && (colSel == null || colSel.getSelected() == null || colSel + .getSelected().size() == 0)) + { + if (!wholewidth && alignment.getWidth() == (1 + sge - sgs)) + { + // do nothing return; - - SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment); - - hideSequence(seqs); - - setSelectionGroup(null); - } - - public void hideSequence(SequenceI [] seq) - { - if(seq!=null) + } + if (colSel == null) { - for (int i = 0; i < seq.length; i++) - alignment.getHiddenSequences().hideSequence(seq[i]); - - hasHiddenRows = true; - firePropertyChange("alignment", null, alignment.getSequences()); + colSel = new ColumnSelection(); + } + for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++) + { + colSel.addElement(cspos); } } - - public void showSequence(int index) - { - Vector tmp = alignment.getHiddenSequences().showSequence(index); - if(tmp.size()>0) + } + + /** + * Returns the (Desktop) instance of the StructureSelectionManager + */ + @Override + public StructureSelectionManager getStructureSelectionManager() + { + return StructureSelectionManager + .getStructureSelectionManager(Desktop.instance); + } + + /** + * + * @param pdbEntries + * @return an array of SequenceI arrays, one for each PDBEntry, listing which + * sequences in the alignment hold a reference to it + */ + public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries) + { + List seqvectors = new ArrayList(); + for (PDBEntry pdb : pdbEntries) + { + List seqs = new ArrayList(); + for (SequenceI sq : alignment.getSequences()) { - if(selectionGroup==null) + Vector pdbs = sq.getDatasetSequence().getAllPDBEntries(); + if (pdbs == null) { - selectionGroup = new SequenceGroup(); - selectionGroup.setEndRes(alignment.getWidth()-1); + continue; } - - for (int t = 0; t < tmp.size(); t++) + for (PDBEntry p1 : pdbs) { - selectionGroup.addSequence( - (SequenceI) tmp.elementAt(t), false - ); + if (p1.getId().equals(pdb.getId())) + { + if (!seqs.contains(sq)) + { + seqs.add(sq); + continue; + } + } } - firePropertyChange("alignment", null, alignment.getSequences()); } - - 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) + seqvectors.add(seqs.toArray(new SequenceI[seqs.size()])); + } + return seqvectors.toArray(new SequenceI[seqvectors.size()][]); + } + + public boolean isNormaliseSequenceLogo() + { + return normaliseSequenceLogo; + } + + public void setNormaliseSequenceLogo(boolean state) + { + normaliseSequenceLogo = state; + } + + /** + * + * @return true if alignment characters should be displayed + */ + public boolean isValidCharWidth() + { + return validCharWidth; + } + + private Hashtable calcIdParams = new Hashtable(); + + public AutoCalcSetting getCalcIdSettingsFor(String calcId) + { + return calcIdParams.get(calcId); + } + + public void setCalcIdSettingsFor(String calcId, AutoCalcSetting settings, + boolean needsUpdate) + { + 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); + } + } + + /** + * 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 command + * @param undo + * @param ssm + */ + @Override + public void mirrorCommand(CommandI command, boolean undo, + StructureSelectionManager ssm, VamsasSource source) + { + /* + * 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(); + } + } + + /** + * 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 al + * @param title + */ + public void addAlignment(AlignmentI al, String title) + { + // 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 + + /* + * If any cDNA/protein mappings can be made between the alignments, offer to + * open a linked alignment with split frame option. + */ + if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true)) + { + if (al.getDataset() == null) { - if(selectionGroup==null) + // need to create ds seqs + for (SequenceI sq : al.getSequences()) { - selectionGroup = new SequenceGroup(); - selectionGroup.setEndRes(alignment.getWidth()-1); + if (sq.getDatasetSequence() == null) + { + sq.createDatasetSequence(); + } } - Vector tmp = alignment.getHiddenSequences().showAll(); - for(int t=0; t 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 + */ + protected boolean openLinkedAlignment(AlignmentI al, String title) + { + 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 = JOptionPane.showOptionDialog(Desktop.desktop, question, + MessageManager.getString("label.open_split_window"), + JOptionPane.DEFAULT_OPTION, JOptionPane.PLAIN_MESSAGE, null, + options, options[0]); - return sequences; + if (response != 1 && response != 2) + { + return false; } + final boolean openSplitPane = (response == 1); + final boolean openInNewWindow = (response == 2); - /** - * 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[] + /* + * Identify protein and dna alignments. Make a copy of this one if opening + * in a new split pane. */ - 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(false); - 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