X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=5a9fa6b044fab2d5c672fa72f00285a5eea8bfaf;hb=10ff37d2cb03f342ddbed679951d3e2fef0a404b;hp=fa458a6ef044899dde24b17588aaeee1e7246a6c;hpb=890bd0eac47a4b0f55bd062a359c16a43c3780a0;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java old mode 100755 new mode 100644 index fa458a6..5a9fa6b --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -1,4 +1,24 @@ /* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) + * Copyright (C) 2014 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) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * @@ -18,111 +38,134 @@ */ 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.AlignmentUtils.MappingResult; +import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; +import jalview.analysis.NJTree; +import jalview.api.AlignViewportI; +import jalview.bin.Cache; +import jalview.commands.CommandI; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.PDBEntry; +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.Color; +import java.awt.Container; +import java.awt.Font; +import java.awt.Rectangle; +import java.util.ArrayDeque; +import java.util.ArrayList; +import java.util.Deque; +import java.util.Hashtable; +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, VamsasSource, AlignViewportI, 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 colourAppliesToAllGroups = true; - ColourSchemeI globalColourScheme = null; - boolean conservationColourSelected = false; - boolean abovePIDThreshold = false; - SequenceGroup selectionGroup; + + SequenceAnnotationOrder sortAnnotationsBy = null; + 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 + /** + * Keys are the feature types which are currently visible. Note: Values are + * not used! + */ 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(); + private Deque historyList = new ArrayDeque(); - Hashtable sequenceColours; + private Deque redoList = new ArrayDeque(); int thresholdTextColour = 0; + Color textColour = Color.black; + Color textColour2 = Color.white; boolean rightAlignIds = false; - Hashtable hiddenRepSequences; - /** * Creates a new AlignViewport object. - * - * @param al DOCUMENT ME! + * + * @param al + * alignment to view */ public AlignViewport(AlignmentI al) { @@ -131,9 +174,42 @@ public class AlignViewport } /** + * 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 + * + * @param al + * AlignmentI + * @param hiddenColumns + * ColumnSelection */ public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns) { @@ -141,10 +217,71 @@ public class AlignViewport if (hiddenColumns != null) { this.colSel = hiddenColumns; - if (hiddenColumns.getHiddenColumns() != null) + if (hiddenColumns.getHiddenColumns() != null + && hiddenColumns.getHiddenColumns().size() > 0) + { + hasHiddenColumns = true; + } + else + { + hasHiddenColumns = false; + } + } + 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) + { + this.colSel = hiddenColumns; + if (hiddenColumns.getHiddenColumns() != null + && hiddenColumns.getHiddenColumns().size() > 0) { hasHiddenColumns = true; } + else + { + hasHiddenColumns = false; + } } init(); } @@ -162,10 +299,12 @@ public class AlignViewport showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true); rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false); - + centreColumnLabels = Cache.getDefault("CENTRE_COLUMN_LABELS", false); autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true); - padGaps = Cache.getDefault("PAD_GAPS", true); + setPadGaps(Cache.getDefault("PAD_GAPS", true)); + shownpfeats = Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true); + showdbrefs = Cache.getDefault("SHOW_DBREFS_TOOLTIP", true); String fontName = Cache.getDefault("FONT_NAME", "SansSerif"); String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + ""); @@ -186,7 +325,8 @@ public class AlignViewport setFont(new Font(fontName, style, Integer.parseInt(fontSize))); - alignment.setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0)); + 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 @@ -194,57 +334,30 @@ public class AlignViewport { 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); - } - } - - consensus = new AlignmentAnnotation("Consensus", "PID", - new Annotation[1], 0f, 100f, - AlignmentAnnotation.BAR_GRAPH); - consensus.hasText = true; - consensus.autoCalculated = true; - - if (Cache.getDefault("SHOW_IDENTITY", true)) - { - alignment.addAnnotation(consensus); + 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); } - + initAutoAnnotation(); if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null) { globalColourScheme = ColourSchemeProperty.getColour(alignment, - jalview.bin.Cache.getProperty("DEFAULT_COLOUR")); + jalview.bin.Cache.getProperty("DEFAULT_COLOUR")); if (globalColourScheme instanceof UserColourScheme) { globalColourScheme = UserDefinedColours.loadDefaultColours(); - ( (UserColourScheme) globalColourScheme).setThreshold(0, - getIgnoreGapsConsensus()); + ((UserColourScheme) globalColourScheme).setThreshold(0, + getIgnoreGapsConsensus()); } if (globalColourScheme != null) @@ -253,13 +366,22 @@ public class AlignViewport } } - wrapAlignment = jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false); + wrapAlignment = Cache.getDefault("WRAP_ALIGNMENT", false); + showUnconserved = 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); } /** - * DOCUMENT ME! - * - * @param b DOCUMENT ME! + * set the flag + * + * @param b + * features are displayed if true */ public void setShowSequenceFeatures(boolean b) { @@ -271,319 +393,22 @@ public class AlignViewport return showSequenceFeatures; } - class ConservationThread - extends Thread - { - AlignmentPanel ap; - public ConservationThread(AlignmentPanel ap) - { - this.ap = ap; - } - - public void run() - { - try - { - updatingConservation = true; - - while (UPDATING_CONSERVATION) - { - try - { - if (ap != null) - { - ap.paintAlignment(true); - } - 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(); - } - - for (int i = 0; i < alWidth; i++) - { - float value = 0; - - c = sequence[i]; - - if (Character.isDigit(c)) - { - value = (int) (c - '0'); - } - else if (c == '*') - { - 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))); - } - } - } - 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); - } - }); - - conservation = null; - quality = null; - - System.out.println("Conservation calculation: " + error); - System.gc(); - - } - - 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; - - /** - * DOCUMENT ME! - */ - public void updateConservation(final AlignmentPanel ap) - { - if (alignment.isNucleotide() || conservation == null) - { - return; - } - - conservationThread = new ConservationThread(ap); - conservationThread.start(); - } - /** - * DOCUMENT ME! + * centre columnar annotation labels in displayed alignment annotation TODO: + * add to jalviewXML and annotation display settings */ - public void updateConsensus(final AlignmentPanel ap) - { - consensusThread = new ConsensusThread(ap); - consensusThread.start(); - } - - class ConsensusThread - extends Thread - { - AlignmentPanel ap; - public ConsensusThread(AlignmentPanel ap) - { - this.ap = ap; - } - - public void run() - { - updatingConsensus = true; - while (UPDATING_CONSENSUS) - { - try - { - if (ap != null) - { - ap.paintAlignment(true); - } - - Thread.sleep(200); - } - catch (Exception ex) - { - ex.printStackTrace(); - } - } - - UPDATING_CONSENSUS = true; - - try - { - int aWidth = alignment.getWidth(); - 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(); - } + boolean centreColumnLabels = false; - String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString(); - String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) + " "; + private boolean showdbrefs; - 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; - javax.swing.SwingUtilities.invokeLater(new Runnable() - { - public void run() - { - 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); - } - }); - - System.out.println("Consensus calculation: " + error); - System.gc(); - } - UPDATING_CONSENSUS = false; - updatingConsensus = false; + private boolean shownpfeats; - if (ap != null) - { - ap.paintAlignment(true); - } - } - } + // --------END Structure Conservation /** - * get the consensus sequence as displayed under the PID consensus annotation row. + * get the consensus sequence as displayed under the PID consensus annotation + * row. + * * @return consensus sequence as a new sequence object */ public SequenceI getConsensusSeq() @@ -613,154 +438,77 @@ public class AlignViewport } SequenceI sq = new Sequence("Consensus", seqs.toString()); - sq.setDescription("Percentage Identity Consensus " + - ( (ignoreGapsInConsensusCalculation) ? " without gaps" : - "")); + sq.setDescription("Percentage Identity Consensus " + + ((ignoreGapsInConsensusCalculation) ? " without gaps" : "")); return sq; } /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ - public SequenceGroup getSelectionGroup() + public int getStartRes() { - return selectionGroup; + return startRes; } /** * DOCUMENT ME! - * - * @param sg DOCUMENT ME! + * + * @return DOCUMENT ME! */ - public void setSelectionGroup(SequenceGroup sg) + public int getEndRes() { - selectionGroup = sg; + return endRes; } /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ - public boolean getConservationSelected() + public int getStartSeq() { - return conservationColourSelected; + return startSeq; } /** * DOCUMENT ME! - * - * @param b DOCUMENT ME! + * + * @param res + * DOCUMENT ME! */ - public void setConservationSelected(boolean b) + public void setStartRes(int res) { - conservationColourSelected = b; + this.startRes = res; } /** * DOCUMENT ME! - * - * @return DOCUMENT ME! + * + * @param seq + * DOCUMENT ME! */ - public boolean getAbovePIDThreshold() + public void setStartSeq(int seq) { - return abovePIDThreshold; + this.startSeq = seq; } /** * DOCUMENT ME! - * - * @param b DOCUMENT ME! + * + * @param res + * DOCUMENT ME! */ - public void setAbovePIDThreshold(boolean b) + public void setEndRes(int res) { - abovePIDThreshold = b; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getStartRes() - { - return startRes; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getEndRes() - { - return endRes; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getStartSeq() - { - return startSeq; - } - - /** - * DOCUMENT ME! - * - * @param cs DOCUMENT ME! - */ - public void setGlobalColourScheme(ColourSchemeI cs) - { - globalColourScheme = cs; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public ColourSchemeI getGlobalColourScheme() - { - return globalColourScheme; - } - - /** - * DOCUMENT ME! - * - * @param res DOCUMENT ME! - */ - public void setStartRes(int res) - { - this.startRes = res; - } - - /** - * DOCUMENT ME! - * - * @param seq DOCUMENT ME! - */ - public void setStartSeq(int seq) - { - this.startSeq = seq; - } - - /** - * DOCUMENT ME! - * - * @param res DOCUMENT ME! - */ - public void setEndRes(int res) - { - if (res > (alignment.getWidth() - 1)) - { - // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1)); - res = alignment.getWidth() - 1; - } + if (res > (alignment.getWidth() - 1)) + { + // log.System.out.println(" Corrected res from " + res + " to maximum " + + // (alignment.getWidth()-1)); + res = alignment.getWidth() - 1; + } if (res < 0) { @@ -772,8 +520,9 @@ public class AlignViewport /** * DOCUMENT ME! - * - * @param seq DOCUMENT ME! + * + * @param seq + * DOCUMENT ME! */ public void setEndSeq(int seq) { @@ -792,7 +541,7 @@ public class AlignViewport /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public int getEndSeq() @@ -802,8 +551,9 @@ public class AlignViewport /** * DOCUMENT ME! - * - * @param f DOCUMENT ME! + * + * @param f + * DOCUMENT ME! */ public void setFont(Font f) { @@ -819,7 +569,7 @@ public class AlignViewport /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public Font getFont() @@ -829,8 +579,9 @@ public class AlignViewport /** * DOCUMENT ME! - * - * @param w DOCUMENT ME! + * + * @param w + * DOCUMENT ME! */ public void setCharWidth(int w) { @@ -839,7 +590,7 @@ public class AlignViewport /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public int getCharWidth() @@ -849,8 +600,9 @@ public class AlignViewport /** * DOCUMENT ME! - * - * @param h DOCUMENT ME! + * + * @param h + * DOCUMENT ME! */ public void setCharHeight(int h) { @@ -859,7 +611,7 @@ public class AlignViewport /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public int getCharHeight() @@ -869,8 +621,9 @@ public class AlignViewport /** * DOCUMENT ME! - * - * @param w DOCUMENT ME! + * + * @param w + * DOCUMENT ME! */ public void setWrappedWidth(int w) { @@ -879,7 +632,7 @@ public class AlignViewport /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public int getWrappedWidth() @@ -889,7 +642,7 @@ public class AlignViewport /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public AlignmentI getAlignment() @@ -899,18 +652,30 @@ public class AlignViewport /** * DOCUMENT ME! - * - * @param align DOCUMENT ME! + * + * @param align + * DOCUMENT ME! */ public void setAlignment(AlignmentI align) { + if (alignment != null && alignment.getCodonFrames() != null) + { + StructureSelectionManager.getStructureSelectionManager( + Desktop.instance).removeMappings(alignment.getCodonFrames()); + } this.alignment = align; + if (alignment != null && alignment.getCodonFrames() != null) + { + StructureSelectionManager.getStructureSelectionManager( + Desktop.instance).addMappings(alignment.getCodonFrames()); + } } /** * DOCUMENT ME! - * - * @param state DOCUMENT ME! + * + * @param state + * DOCUMENT ME! */ public void setWrapAlignment(boolean state) { @@ -919,8 +684,9 @@ public class AlignViewport /** * DOCUMENT ME! - * - * @param state DOCUMENT ME! + * + * @param state + * DOCUMENT ME! */ public void setShowText(boolean state) { @@ -929,8 +695,9 @@ public class AlignViewport /** * DOCUMENT ME! - * - * @param state DOCUMENT ME! + * + * @param state + * DOCUMENT ME! */ public void setRenderGaps(boolean state) { @@ -939,7 +706,7 @@ public class AlignViewport /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public boolean getColourText() @@ -949,8 +716,9 @@ public class AlignViewport /** * DOCUMENT ME! - * - * @param state DOCUMENT ME! + * + * @param state + * DOCUMENT ME! */ public void setColourText(boolean state) { @@ -959,8 +727,9 @@ public class AlignViewport /** * DOCUMENT ME! - * - * @param state DOCUMENT ME! + * + * @param state + * DOCUMENT ME! */ public void setShowBoxes(boolean state) { @@ -969,7 +738,7 @@ public class AlignViewport /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public boolean getWrapAlignment() @@ -979,7 +748,7 @@ public class AlignViewport /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public boolean getShowText() @@ -989,7 +758,7 @@ public class AlignViewport /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public boolean getShowBoxes() @@ -999,7 +768,7 @@ public class AlignViewport /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public char getGapCharacter() @@ -1009,8 +778,9 @@ public class AlignViewport /** * DOCUMENT ME! - * - * @param gap DOCUMENT ME! + * + * @param gap + * DOCUMENT ME! */ public void setGapCharacter(char gap) { @@ -1022,47 +792,7 @@ public class AlignViewport /** * 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() @@ -1072,8 +802,9 @@ public class AlignViewport /** * DOCUMENT ME! - * - * @param tree DOCUMENT ME! + * + * @param tree + * DOCUMENT ME! */ public void setCurrentTree(NJTree tree) { @@ -1082,7 +813,7 @@ public class AlignViewport /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public NJTree getCurrentTree() @@ -1092,27 +823,7 @@ public class AlignViewport /** * 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() @@ -1122,8 +833,9 @@ public class AlignViewport /** * DOCUMENT ME! - * - * @param b DOCUMENT ME! + * + * @param b + * DOCUMENT ME! */ public void setShowJVSuffix(boolean b) { @@ -1132,7 +844,7 @@ public class AlignViewport /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public boolean getShowAnnotation() @@ -1142,8 +854,9 @@ public class AlignViewport /** * DOCUMENT ME! - * - * @param b DOCUMENT ME! + * + * @param b + * DOCUMENT ME! */ public void setShowAnnotation(boolean b) { @@ -1152,7 +865,7 @@ public class AlignViewport /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public boolean getScaleAboveWrapped() @@ -1162,7 +875,7 @@ public class AlignViewport /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public boolean getScaleLeftWrapped() @@ -1172,7 +885,7 @@ public class AlignViewport /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public boolean getScaleRightWrapped() @@ -1182,8 +895,9 @@ public class AlignViewport /** * DOCUMENT ME! - * - * @param b DOCUMENT ME! + * + * @param b + * DOCUMENT ME! */ public void setScaleAboveWrapped(boolean b) { @@ -1192,8 +906,9 @@ public class AlignViewport /** * DOCUMENT ME! - * - * @param b DOCUMENT ME! + * + * @param b + * DOCUMENT ME! */ public void setScaleLeftWrapped(boolean b) { @@ -1202,603 +917,684 @@ public class AlignViewport /** * DOCUMENT ME! - * - * @param 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) + public void setDataset(boolean b) { - changeSupport.addPropertyChangeListener(listener); + isDataset = b; + } + + public boolean isDataset() + { + return isDataset; + } + + public boolean getShowHiddenMarkers() + { + return showHiddenMarkers; + } + + public void setShowHiddenMarkers(boolean show) + { + showHiddenMarkers = show; } /** - * DOCUMENT ME! - * - * @param listener DOCUMENT ME! + * returns the visible column regions of the alignment + * + * @param selectedRegionOnly + * true to just return the contigs intersecting with the selected + * area + * @return */ - public void removePropertyChangeListener( - java.beans.PropertyChangeListener listener) + public int[] getViewAsVisibleContigs(boolean selectedRegionOnly) { - changeSupport.removePropertyChangeListener(listener); + 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; } /** - * Property change listener for changes in alignment - * - * @param prop DOCUMENT ME! - * @param oldvalue DOCUMENT ME! - * @param newvalue DOCUMENT ME! + * get hash of undo and redo list for the alignment + * + * @return long[] { historyList.hashCode, redoList.hashCode }; */ - public void firePropertyChange(String prop, Object oldvalue, Object newvalue) + public long[] getUndoRedoHash() { - changeSupport.firePropertyChange(prop, oldvalue, newvalue); + // TODO: JAL-1126 + if (historyList == null || redoList == null) + { + return new long[] + { -1, -1 }; + } + return new long[] + { historyList.hashCode(), this.redoList.hashCode() }; } - public void setIgnoreGapsConsensus(boolean b, 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) { - ignoreGapsInConsensusCalculation = b; - updateConsensus(ap); - if (globalColourScheme != null) + if (undoredo == null) + { + return true; + } + long[] cstate = getUndoRedoHash(); + if (cstate.length != undoredo.length) { - globalColourScheme.setThreshold(globalColourScheme.getThreshold(), - ignoreGapsInConsensusCalculation); + return true; + } + + for (int i = 0; i < cstate.length; i++) + { + if (cstate[i] != undoredo[i]) + { + return true; + } } + return false; } - public boolean getIgnoreGapsConsensus() + public boolean getCentreColumnLabels() { - return ignoreGapsInConsensusCalculation; + return centreColumnLabels; } - public void setDataset(boolean b) + public void setCentreColumnLabels(boolean centrecolumnlabels) { - isDataset = b; + centreColumnLabels = centrecolumnlabels; } - public boolean isDataset() + /** + * enable or disable the display of Database Cross References in the sequence + * ID tooltip + */ + public void setShowDbRefs(boolean show) { - return isDataset; + showdbrefs = show; } - public void hideSelectedColumns() + /** + * + * @return true if Database References are to be displayed on tooltips. + */ + public boolean isShowDbRefs() { - if (colSel.size() < 1) - { - return; - } - - colSel.hideSelectedColumns(); - setSelectionGroup(null); + return showdbrefs; + } - hasHiddenColumns = true; + /** + * + * @return true if Non-positional features are to be displayed on tooltips. + */ + public boolean isShowNpFeats() + { + return shownpfeats; } - public void hideColumns(int start, int end) + /** + * enable or disable the display of Non-Positional sequence features in the + * sequence ID tooltip + * + * @param show + */ + public void setShowNpFeats(boolean show) { - if (start == end) - { - colSel.hideColumns(start); - } - else - { - colSel.hideColumns(start, end); - } + shownpfeats = show; + } - hasHiddenColumns = true; + /** + * + * @return true if view has hidden rows + */ + public boolean hasHiddenRows() + { + return hasHiddenRows; } - public void hideRepSequences(SequenceI repSequence, SequenceGroup sg) + /** + * + * @return true if view has hidden columns + */ + public boolean hasHiddenColumns() { - int sSize = sg.getSize(); - if (sSize < 2) - { - return; - } + return hasHiddenColumns; + } - if (hiddenRepSequences == null) - { - hiddenRepSequences = new Hashtable(); - } + /** + * when set, view will scroll to show the highlighted position + */ + public boolean followHighlight = true; - hiddenRepSequences.put(repSequence, sg); + /** + * @return true if view should scroll to show the highlighted region of a + * sequence + * @return + */ + public boolean getFollowHighlight() + { + return followHighlight; + } - //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; - } + public boolean followSelection = true; - seqs[index++] = sg.getSequenceAt(i); - } - } + /** + * @return true if view selection should always follow the selections + * broadcast by other selection sources + */ + public boolean getFollowSelection() + { + return followSelection; + } - hideSequence(seqs); + boolean showSeqFeaturesHeight; + /** + * 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); } - public void hideAllSelectedSeqs() + public void setShowSequenceFeaturesHeight(boolean selected) { - if (selectionGroup == null || selectionGroup.getSize()<1) - { - return; - } - - SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment); - - hideSequence(seqs); - - setSelectionGroup(null); + showSeqFeaturesHeight = selected; } - public void hideSequence(SequenceI[] seq) + public boolean getShowSequenceFeaturesHeight() { - if (seq != null) - { - for (int i = 0; i < seq.length; i++) - { - alignment.getHiddenSequences().hideSequence(seq[i]); - } - hasHiddenRows = true; - firePropertyChange("alignment", null, alignment.getSequences()); - } + return showSeqFeaturesHeight; } - public void showSequence(int index) + /** + * 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() { - Vector tmp = alignment.getHiddenSequences().showSequence(index - , hiddenRepSequences); - if (tmp.size() > 0) + AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(this + .getSequenceSetId()); + AlignmentPanel ap = null; + for (int p = 0; aps != null && p < aps.length; p++) { - if (selectionGroup == null) + if (aps[p].av == this) { - selectionGroup = new SequenceGroup(); - selectionGroup.setEndRes(alignment.getWidth() - 1); + return aps[p]; } - - for (int t = 0; t < tmp.size(); t++) - { - selectionGroup.addSequence( - (SequenceI) tmp.elementAt(t), false - ); - } - firePropertyChange("alignment", null, alignment.getSequences()); - } - - if (alignment.getHiddenSequences().getSize() < 1) - { - hasHiddenRows = false; } + return null; } - public void showColumn(int col) + public boolean getSortByTree() { - colSel.revealHiddenColumns(col); - if (colSel.getHiddenColumns() == null) - { - hasHiddenColumns = false; - } + return sortByTree; } - public void showAllHiddenColumns() + public void setSortByTree(boolean sort) { - colSel.revealAllHiddenColumns(); - hasHiddenColumns = false; + sortByTree = sort; } - public void showAllHiddenSeqs() + /** + * 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) { - if (alignment.getHiddenSequences().getSize() > 0) + 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 (selectionGroup == null) + if (!wholewidth && alignment.getWidth() == (1 + sge - sgs)) { - selectionGroup = new SequenceGroup(); - selectionGroup.setEndRes(alignment.getWidth() - 1); + // do nothing + return; } - Vector tmp = alignment.getHiddenSequences().showAll(hiddenRepSequences); - for (int t = 0; t < tmp.size(); t++) + if (colSel == null) { - selectionGroup.addSequence( - (SequenceI) tmp.elementAt(t), false - ); + colSel = new ColumnSelection(); + } + for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++) + { + colSel.addElement(cspos); } - firePropertyChange("alignment", null, alignment.getSequences()); - hasHiddenRows = false; - hiddenRepSequences = null; } } - public void invertColumnSelection() + public StructureSelectionManager getStructureSelectionManager() + { + return StructureSelectionManager + .getStructureSelectionManager(Desktop.instance); + } + + /** + * + * @param pdbEntries + * @return a series of SequenceI arrays, one for each PDBEntry, listing which + * sequence in the alignment holds a reference to it + */ + public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries) { - for (int i = 0; i < alignment.getWidth(); i++) + ArrayList seqvectors = new ArrayList(); + for (PDBEntry pdb : pdbEntries) { - if (colSel.contains(i)) - { - colSel.removeElement(i); - } - else + ArrayList seqs = new ArrayList(); + for (int i = 0; i < alignment.getHeight(); i++) { - if (!hasHiddenColumns || colSel.isVisible(i)) + Vector pdbs = alignment.getSequenceAt(i).getDatasetSequence() + .getPDBId(); + if (pdbs == null) { - colSel.addElement(i); + continue; + } + SequenceI sq; + for (int p = 0; p < pdbs.size(); p++) + { + PDBEntry p1 = (PDBEntry) pdbs.elementAt(p); + if (p1.getId().equals(pdb.getId())) + { + if (!seqs.contains(sq = alignment.getSequenceAt(i))) + { + seqs.add(sq); + } + + continue; + } } } + seqvectors.add(seqs.toArray(new SequenceI[seqs.size()])); } + return seqvectors.toArray(new SequenceI[seqvectors.size()][]); + } + + public boolean isNormaliseSequenceLogo() + { + return normaliseSequenceLogo; } - public int adjustForHiddenSeqs(int alignmentIndex) + public void setNormaliseSequenceLogo(boolean state) { - return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex); + normaliseSequenceLogo = state; } /** - * This method returns the a new SequenceI [] with - * the selection sequence and start and end points adjusted - * @return String[] + * + * @return true if alignment characters should be displayed */ - public SequenceI[] getSelectionAsNewSequence() + public boolean isValidCharWidth() { - SequenceI[] sequences; + return validCharWidth; + } - if (selectionGroup == null) - { - sequences = alignment.getSequencesArray(); - } - else + private Hashtable calcIdParams = new Hashtable(); + + private boolean showAutocalculatedAbove; + + 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) { - sequences = selectionGroup.getSelectionAsNewSequences(alignment); + Cache.log.debug("trigger update for " + calcId); } + } - return sequences; + protected SequenceAnnotationOrder getSortAnnotationsBy() + { + return sortAnnotationsBy; } - /** - * 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) + protected void setSortAnnotationsBy(SequenceAnnotationOrder sortAnnotationsBy) { - CigarArray selection = null; - SequenceI[] seqs = null; - int i, iSize; - int start = 0, end = 0; - if (selectedRegionOnly && selectionGroup != null) + this.sortAnnotationsBy = sortAnnotationsBy; + } + + protected boolean isShowAutocalculatedAbove() + { + return showAutocalculatedAbove; + } + + protected void setShowAutocalculatedAbove(boolean showAutocalculatedAbove) + { + this.showAutocalculatedAbove = showAutocalculatedAbove; + } + + /** + * 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) + { + /* + * ...work in progress... 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) { - iSize = selectionGroup.getSize(); - seqs = selectionGroup.getSequencesInOrder(alignment); - start = selectionGroup.getStartRes(); - end = selectionGroup.getEndRes(); // inclusive for start and end in SeqCigar constructor + // ok to continue; } 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); + return; } - 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 + CommandI mappedCommand = ssm.mapCommand(command, undo, getAlignment(), + getGapCharacter()); + if (mappedCommand != null) { - selection.addOperation(CigarArray.M, end - start + 1); + AlignmentI[] views = getAlignPanel().alignFrame.getViewAlignments(); + mappedCommand.doCommand(views); + getAlignPanel().alignmentChanged(); } - return selection; + } + + @Override + public VamsasSource getVamsasSource() + { + return this; } /** - * 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 + * Add one command to the command history list. + * + * @param command */ - jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly) + public void addToHistoryList(CommandI command) { - // 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) + if (this.historyList != null) { - return new AlignmentView(aligview, - (selectedOnly && selectionGroup != null) ? - selectionGroup.getStartRes() : 0); + this.historyList.push(command); + broadcastCommand(command, false); } - return null; + } + + protected void broadcastCommand(CommandI command, boolean undo) + { + getStructureSelectionManager().commandPerformed(command, undo, getVamsasSource()); } /** - * 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[] + * Add one command to the command redo list. + * + * @param command */ - public String[] getViewAsString(boolean selectedRegionOnly) + public void addToRedoList(CommandI command) { - 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 + if (this.redoList != null) { - iSize = alignment.getHeight(); - seqs = alignment.getSequencesArray(); - end = alignment.getWidth(); + this.redoList.push(command); } - - 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; + broadcastCommand(command, true); } - public int [][] getVisibleRegionBoundaries(int min, int max) + /** + * Clear the command redo list. + */ + public void clearRedoList() { - Vector regions = new Vector(); - int start = min; - int end = max; - - do + if (this.redoList != null) { - 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; - } + this.redoList.clear(); } - while (end < max); - - int[][] startEnd = new int[regions.size()][2]; - - regions.copyInto(startEnd); - - return startEnd; - } - public boolean getShowHiddenMarkers() + public void setHistoryList(Deque list) { - return showHiddenMarkers; + this.historyList = list; } - public void setShowHiddenMarkers(boolean show) + public Deque getHistoryList() { - showHiddenMarkers = show; + return this.historyList; } - public String getSequenceSetId() + public void setRedoList(Deque list) { - if (sequenceSetID == null) - { - sequenceSetID = alignment.hashCode() + ""; - } + this.redoList = list; + } - return sequenceSetID; + public Deque getRedoList() + { + return this.redoList; } - public void alignmentChanged(AlignmentPanel ap) + /** + * 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) { - if (padGaps) - { - alignment.padGaps(); - } + // TODO: promote to AlignViewportI? applet CutAndPasteTransfer is different - if (hconsensus != null && autoCalculateConsensus) - { - updateConsensus(ap); - updateConservation(ap); - } + // refactored from FileLoader / CutAndPasteTransfer / SequenceFetcher with + // this comment: + // TODO: create undo object for this JAL-1101 - //Reset endRes of groups if beyond alignment width - int alWidth = alignment.getWidth(); - Vector groups = alignment.getGroups(); - if (groups != null) + /* + * If one alignment is protein and one nucleotide, with at least one + * sequence name in common, offer to open a linked alignment. + */ + if (getAlignment().isNucleotide() != al.isNucleotide()) { - for (int i = 0; i < groups.size(); i++) + final Set sequenceNames = getAlignment().getSequenceNames(); + sequenceNames.retainAll(al.getSequenceNames()); + if (!sequenceNames.isEmpty()) // at least one sequence name in both { - SequenceGroup sg = (SequenceGroup) groups.elementAt(i); - if (sg.getEndRes() > alWidth) + if (openLinkedAlignment(al, title)) { - sg.setEndRes(alWidth - 1); + return; } } } - if (selectionGroup != null && selectionGroup.getEndRes() > alWidth) + for (int i = 0; i < al.getHeight(); i++) { - selectionGroup.setEndRes(alWidth - 1); + getAlignment().addSequence(al.getSequenceAt(i)); } - - resetAllColourSchemes(); - - // alignment.adjustSequenceAnnotations(); + // TODO this call was done by SequenceFetcher but not FileLoader or + // CutAndPasteTransfer. Is it needed? + setEndSeq(getAlignment().getHeight()); + firePropertyChange("alignment", null, getAlignment().getSequences()); } - void resetAllColourSchemes() + /** + * Show a dialog with the option to open and link (cDNA <-> protein) as a new + * alignment. Returns true if the new alignment was opened, false if not, + * because the user declined the offer. + * + * @param title + */ + protected boolean openLinkedAlignment(AlignmentI al, String title) { - ColourSchemeI cs = globalColourScheme; - if (cs != null) - { - if (cs instanceof ClustalxColourScheme) - { - ( (ClustalxColourScheme) cs). - resetClustalX(alignment.getSequences(), - alignment.getWidth()); - } + 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_linked_alignment?")); + int response = JOptionPane.showOptionDialog(Desktop.desktop, question, + MessageManager.getString("label.open_linked_alignment"), + JOptionPane.DEFAULT_OPTION, JOptionPane.PLAIN_MESSAGE, null, + options, options[0]); - 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); - } + if (response != 1 && response != 2) + { + return false; } - - int s, sSize = alignment.getGroups().size(); - for (s = 0; s < sSize; s++) + final boolean openSplitPane = (response == 1); + final boolean openInNewWindow = (response == 2); + + /* + * Create the AlignFrame first (which creates the new alignment's datasets), + * before attempting sequence mapping. + */ + AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT); + + /* + * 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(); + final AlignmentI protein = al.isNucleotide() ? thisAlignment : al; + final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment; + + newAlignFrame.statusBar.setText(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(AppletFormatAdapter.PASTE)) + // { + // alignFrame.setFileName(file, format); + // } + + if (openInNewWindow) { - 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(); + Desktop.addInternalFrame(newAlignFrame, title, + AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT); } - } - public Color getSequenceColour(SequenceI seq) - { - if (sequenceColours == null || !sequenceColours.containsKey(seq)) + /* + * Try to find mappings for at least one sequence. + */ + MappingResult mapped = AlignmentUtils.mapProteinToCdna(protein, cdna); + final StructureSelectionManager ssm = StructureSelectionManager + .getStructureSelectionManager(Desktop.instance); + if (mapped == MappingResult.Mapped) { - return Color.white; + + /* + * Register the mappings (held on the protein alignment) with the + * StructureSelectionManager (for mouseover linking). + */ + ssm.addMappings(protein.getCodonFrames()); } else { - return (Color) sequenceColours.get(seq); - } - } - public void setSequenceColour(SequenceI seq, Color col) - { - if (sequenceColours == null) - { - sequenceColours = new Hashtable(); + /* + * No mapping possible - warn the user, but leave window open. + */ + final String msg = JvSwingUtils.wrapTooltip(true, + MessageManager.getString("label.mapping_failed")); + JOptionPane.showInternalMessageDialog(Desktop.desktop, msg, + MessageManager.getString("label.no_mappings"), + JOptionPane.WARNING_MESSAGE); } - if (col == null) + try + { + newAlignFrame.setMaximum(jalview.bin.Cache.getDefault( + "SHOW_FULLSCREEN", + false)); + } catch (java.beans.PropertyVetoException ex) { - sequenceColours.remove(seq); } - else + + if (openSplitPane) { - sequenceColours.put(seq, col); + /* + * Open in split pane. DNA sequence above, protein below. + */ + AlignFrame copyMe = new AlignFrame(thisAlignment, + AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); + copyMe.setTitle(""); // TODO would like this AlignFrame.title here + final AlignFrame proteinFrame = al.isNucleotide() ? copyMe + : newAlignFrame; + final AlignFrame cdnaFrame = al.isNucleotide() ? newAlignFrame + : copyMe; + newAlignFrame.setTitle(title); + + cdnaFrame.setVisible(true); + proteinFrame.setVisible(true); + JInternalFrame splitFrame = new SplitFrame(cdnaFrame, proteinFrame); + Desktop.addInternalFrame(splitFrame, title, AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT); + + /* + * Set the frames to list for each other's edit and sort commands. + */ + ssm.addCommandListener(cdnaFrame.getViewport()); + ssm.addCommandListener(proteinFrame.getViewport()); + + /* + * cDNA view will mirror edits, selection, sorting, show/hide on protein + */ + proteinFrame.getViewport().setCodingComplement(cdnaFrame.getViewport()); } - } + return true; + } }