X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=5a9fa6b044fab2d5c672fa72f00285a5eea8bfaf;hb=10ff37d2cb03f342ddbed679951d3e2fef0a404b;hp=9f1d3c685195a5e871d20d1e46753db5fb1eaeab;hpb=1576c6118a09c59098483daa16a94e9cca8de260;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java old mode 100755 new mode 100644 index 9f1d3c6..5a9fa6b --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -1,20 +1,22 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) + * Copyright (C) 2014 The Jalview Authors * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. + * This file is part of Jalview. * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. + * Jalview is 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ /* * Jalview - A Sequence Alignment Editor and Viewer @@ -36,26 +38,52 @@ */ 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; @@ -81,15 +109,7 @@ public class AlignViewport boolean showAnnotation = true; - boolean colourAppliesToAllGroups = true; - - ColourSchemeI globalColourScheme = null; - - boolean conservationColourSelected = false; - - boolean abovePIDThreshold = false; - - SequenceGroup selectionGroup; + SequenceAnnotationOrder sortAnnotationsBy = null; int charHeight; @@ -103,14 +123,6 @@ public class AlignViewport boolean seqNameItalics; - AlignmentI alignment; - - ColumnSelection colSel = new ColumnSelection(); - - int threshold; - - int increment; - NJTree currentTree = null; boolean scaleAboveWrapped = false; @@ -119,57 +131,27 @@ public class AlignViewport 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; @@ -179,13 +161,11 @@ public class AlignViewport boolean rightAlignIds = false; - Hashtable hiddenRepSequences; - /** * Creates a new AlignViewport object. * * @param al - * DOCUMENT ME! + * alignment to view */ public AlignViewport(AlignmentI al) { @@ -194,12 +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 + * AlignmentI * @param hiddenColumns - * ColumnSelection + * ColumnSelection */ public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns) { @@ -207,10 +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(); } @@ -231,10 +302,10 @@ public class AlignViewport centreColumnLabels = Cache.getDefault("CENTRE_COLUMN_LABELS", false); autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true); - padGaps = Cache.getDefault("PAD_GAPS", true); - shownpfeats = Cache.getDefault("SHOW_NPFEATS_TOOLTIP",true); - showdbrefs = Cache.getDefault("SHOW_DBREFS_TOOLTIP",true); - + setPadGaps(Cache.getDefault("PAD_GAPS", true)); + 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 + ""); String fontSize = Cache.getDefault("FONT_SIZE", "10"); @@ -263,41 +334,20 @@ 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, @@ -316,14 +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! + * set the flag * * @param b - * DOCUMENT ME! + * features are displayed if true */ public void setShowSequenceFeatures(boolean b) { @@ -335,160 +393,6 @@ 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(false); - } - Thread.sleep(200); - } catch (Exception ex) - { - ex.printStackTrace(); - } - } - - UPDATING_CONSERVATION = true; - - int alWidth = alignment.getWidth(); - if (alWidth < 0) - { - return; - } - - Conservation cons = new jalview.analysis.Conservation("All", - jalview.schemes.ResidueProperties.propHash, 3, alignment - .getSequences(), 0, alWidth - 1); - - cons.calculate(); - cons.verdict(false, ConsPercGaps); - - if (quality != null) - { - cons.findQuality(); - } - - char[] sequence = cons.getConsSequence().getSequence(); - float minR; - float minG; - float minB; - float maxR; - float maxG; - float maxB; - minR = 0.3f; - minG = 0.0f; - minB = 0f; - maxR = 1.0f - minR; - maxG = 0.9f - minG; - maxB = 0f - minB; // scalable range for colouring both Conservation and - // Quality - - float min = 0f; - float max = 11f; - float qmin = 0f; - float qmax = 0f; - - char c; - - conservation.annotations = new Annotation[alWidth]; - - if (quality != null) - { - quality.graphMax = cons.qualityRange[1].floatValue(); - quality.annotations = new Annotation[alWidth]; - qmin = cons.qualityRange[0].floatValue(); - qmax = cons.qualityRange[1].floatValue(); - } - - 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) - { - new OOMWarning("calculating conservation", error); - - conservation = null; - quality = null; - - } - - UPDATING_CONSERVATION = false; - updatingConservation = false; - - if (ap != null) - { - ap.paintAlignment(true); - } - - } - } - - ConservationThread conservationThread; - - ConsensusThread consensusThread; - - boolean consUpdateNeeded = false; - - static boolean UPDATING_CONSENSUS = false; - - static boolean UPDATING_CONSERVATION = false; - - boolean updatingConsensus = false; - - boolean updatingConservation = false; - /** * centre columnar annotation labels in displayed alignment annotation TODO: * add to jalviewXML and annotation display settings @@ -499,129 +403,7 @@ public class AlignViewport private boolean shownpfeats; - /** - * trigger update of conservation annotation - */ - public void updateConservation(final AlignmentPanel ap) - { - if (alignment.isNucleotide() || conservation == null) - { - return; - } - - conservationThread = new ConservationThread(ap); - conservationThread.start(); - } - - /** - * trigger update of consensus annotation - */ - 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(false); - } - - Thread.sleep(200); - } catch (Exception ex) - { - ex.printStackTrace(); - } - } - - UPDATING_CONSENSUS = true; - - try - { - int aWidth = (alignment != null) ? alignment.getWidth() : 0; // null - // pointer - // possibility - // here. - if (aWidth < 0) - { - return; - } - - consensus.annotations = null; - consensus.annotations = new Annotation[aWidth]; - - hconsensus = new Hashtable[aWidth]; - AAFrequency.calculate(alignment.getSequencesArray(), 0, alignment - .getWidth(), hconsensus); - - for (int i = 0; i < aWidth; i++) - { - float value = 0; - if (ignoreGapsInConsensusCalculation) - { - value = ((Float) hconsensus[i].get(AAFrequency.PID_NOGAPS)) - .floatValue(); - } - else - { - value = ((Float) hconsensus[i].get(AAFrequency.PID_GAPS)) - .floatValue(); - } - - String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE) - .toString(); - String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) - + " "; - - if (maxRes.length() > 1) - { - mouseOver = "[" + maxRes + "] "; - maxRes = "+"; - } - - mouseOver += ((int) value + "%"); - consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ', - value); - } - - if (globalColourScheme != null) - { - globalColourScheme.setConsensus(hconsensus); - } - - } catch (OutOfMemoryError error) - { - alignment.deleteAnnotation(consensus); - - consensus = null; - hconsensus = null; - new OOMWarning("calculating consensus", error); - } - UPDATING_CONSENSUS = false; - updatingConsensus = false; - - if (ap != null) - { - ap.paintAlignment(true); - } - } - } + // --------END Structure Conservation /** * get the consensus sequence as displayed under the PID consensus annotation @@ -666,20 +448,19 @@ public class AlignViewport * * @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; } /** @@ -687,130 +468,47 @@ public class AlignViewport * * @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) { @@ -824,7 +522,7 @@ public class AlignViewport * DOCUMENT ME! * * @param seq - * DOCUMENT ME! + * DOCUMENT ME! */ public void setEndSeq(int seq) { @@ -855,7 +553,7 @@ public class AlignViewport * DOCUMENT ME! * * @param f - * DOCUMENT ME! + * DOCUMENT ME! */ public void setFont(Font f) { @@ -883,7 +581,7 @@ public class AlignViewport * DOCUMENT ME! * * @param w - * DOCUMENT ME! + * DOCUMENT ME! */ public void setCharWidth(int w) { @@ -904,7 +602,7 @@ public class AlignViewport * DOCUMENT ME! * * @param h - * DOCUMENT ME! + * DOCUMENT ME! */ public void setCharHeight(int h) { @@ -925,7 +623,7 @@ public class AlignViewport * DOCUMENT ME! * * @param w - * DOCUMENT ME! + * DOCUMENT ME! */ public void setWrappedWidth(int w) { @@ -956,20 +654,20 @@ public class AlignViewport * DOCUMENT ME! * * @param align - * DOCUMENT ME! + * DOCUMENT ME! */ public void setAlignment(AlignmentI align) { if (alignment != null && alignment.getCodonFrames() != null) { - StructureSelectionManager.getStructureSelectionManager() - .removeMappings(alignment.getCodonFrames()); + StructureSelectionManager.getStructureSelectionManager( + Desktop.instance).removeMappings(alignment.getCodonFrames()); } this.alignment = align; - if (alignment.getCodonFrames() != null) + if (alignment != null && alignment.getCodonFrames() != null) { - StructureSelectionManager.getStructureSelectionManager().addMappings( - alignment.getCodonFrames()); + StructureSelectionManager.getStructureSelectionManager( + Desktop.instance).addMappings(alignment.getCodonFrames()); } } @@ -977,7 +675,7 @@ public class AlignViewport * DOCUMENT ME! * * @param state - * DOCUMENT ME! + * DOCUMENT ME! */ public void setWrapAlignment(boolean state) { @@ -988,7 +686,7 @@ public class AlignViewport * DOCUMENT ME! * * @param state - * DOCUMENT ME! + * DOCUMENT ME! */ public void setShowText(boolean state) { @@ -999,7 +697,7 @@ public class AlignViewport * DOCUMENT ME! * * @param state - * DOCUMENT ME! + * DOCUMENT ME! */ public void setRenderGaps(boolean state) { @@ -1020,7 +718,7 @@ public class AlignViewport * DOCUMENT ME! * * @param state - * DOCUMENT ME! + * DOCUMENT ME! */ public void setColourText(boolean state) { @@ -1031,7 +729,7 @@ public class AlignViewport * DOCUMENT ME! * * @param state - * DOCUMENT ME! + * DOCUMENT ME! */ public void setShowBoxes(boolean state) { @@ -1082,7 +780,7 @@ public class AlignViewport * DOCUMENT ME! * * @param gap - * DOCUMENT ME! + * DOCUMENT ME! */ public void setGapCharacter(char gap) { @@ -1095,48 +793,6 @@ 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() @@ -1148,7 +804,7 @@ public class AlignViewport * DOCUMENT ME! * * @param tree - * DOCUMENT ME! + * DOCUMENT ME! */ public void setCurrentTree(NJTree tree) { @@ -1168,27 +824,6 @@ 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() @@ -1200,7 +835,7 @@ public class AlignViewport * DOCUMENT ME! * * @param b - * DOCUMENT ME! + * DOCUMENT ME! */ public void setShowJVSuffix(boolean b) { @@ -1221,7 +856,7 @@ public class AlignViewport * DOCUMENT ME! * * @param b - * DOCUMENT ME! + * DOCUMENT ME! */ public void setShowAnnotation(boolean b) { @@ -1262,7 +897,7 @@ public class AlignViewport * DOCUMENT ME! * * @param b - * DOCUMENT ME! + * DOCUMENT ME! */ public void setScaleAboveWrapped(boolean b) { @@ -1273,7 +908,7 @@ public class AlignViewport * DOCUMENT ME! * * @param b - * DOCUMENT ME! + * DOCUMENT ME! */ public void setScaleLeftWrapped(boolean b) { @@ -1284,69 +919,13 @@ public class AlignViewport * DOCUMENT ME! * * @param b - * DOCUMENT ME! + * DOCUMENT ME! */ public void setScaleRightWrapped(boolean b) { scaleRightWrapped = b; } - /** - * Property change listener for changes in alignment - * - * @param listener - * DOCUMENT ME! - */ - public void addPropertyChangeListener( - java.beans.PropertyChangeListener listener) - { - changeSupport.addPropertyChangeListener(listener); - } - - /** - * DOCUMENT ME! - * - * @param listener - * DOCUMENT ME! - */ - public void removePropertyChangeListener( - java.beans.PropertyChangeListener listener) - { - changeSupport.removePropertyChangeListener(listener); - } - - /** - * Property change listener for changes in alignment - * - * @param prop - * DOCUMENT ME! - * @param oldvalue - * DOCUMENT ME! - * @param newvalue - * DOCUMENT ME! - */ - public void firePropertyChange(String prop, Object oldvalue, - Object newvalue) - { - changeSupport.firePropertyChange(prop, oldvalue, newvalue); - } - - public void setIgnoreGapsConsensus(boolean b, AlignmentPanel ap) - { - ignoreGapsInConsensusCalculation = b; - updateConsensus(ap); - if (globalColourScheme != null) - { - globalColourScheme.setThreshold(globalColourScheme.getThreshold(), - ignoreGapsInConsensusCalculation); - } - } - - public boolean getIgnoreGapsConsensus() - { - return ignoreGapsInConsensusCalculation; - } - public void setDataset(boolean b) { isDataset = b; @@ -1357,687 +936,665 @@ public class AlignViewport return isDataset; } - public void hideSelectedColumns() + public boolean getShowHiddenMarkers() { - if (colSel.size() < 1) - { - return; - } - - colSel.hideSelectedColumns(); - setSelectionGroup(null); + return showHiddenMarkers; + } - hasHiddenColumns = true; + public void setShowHiddenMarkers(boolean show) + { + showHiddenMarkers = show; } - public void hideColumns(int start, int end) + /** + * 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) { - if (start == end) + int[] viscontigs = null; + int start = 0, end = 0; + if (selectedRegionOnly && selectionGroup != null) { - colSel.hideColumns(start); + start = selectionGroup.getStartRes(); + end = selectionGroup.getEndRes() + 1; } else { - colSel.hideColumns(start, end); + end = alignment.getWidth(); } - - hasHiddenColumns = true; + viscontigs = colSel.getVisibleContigs(start, end); + return viscontigs; } - public void hideRepSequences(SequenceI repSequence, SequenceGroup sg) + /** + * get hash of undo and redo list for the alignment + * + * @return long[] { historyList.hashCode, redoList.hashCode }; + */ + public long[] getUndoRedoHash() { - int sSize = sg.getSize(); - if (sSize < 2) - { - return; - } - - if (hiddenRepSequences == null) - { - hiddenRepSequences = new Hashtable(); - } - - hiddenRepSequences.put(repSequence, sg); - - // Hide all sequences except the repSequence - SequenceI[] seqs = new SequenceI[sSize - 1]; - int index = 0; - for (int i = 0; i < sSize; i++) + // TODO: JAL-1126 + if (historyList == null || redoList == null) { - if (sg.getSequenceAt(i) != repSequence) - { - if (index == sSize - 1) - { - return; - } - - seqs[index++] = sg.getSequenceAt(i); - } + return new long[] + { -1, -1 }; } - - hideSequence(seqs); - + return new long[] + { historyList.hashCode(), this.redoList.hashCode() }; } - public void hideAllSelectedSeqs() + /** + * 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 (selectionGroup == null || selectionGroup.getSize() < 1) + if (undoredo == null) { - return; + return true; } - - SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment); - - hideSequence(seqs); - - setSelectionGroup(null); - } - - public void hideSequence(SequenceI[] seq) - { - if (seq != null) + long[] cstate = getUndoRedoHash(); + if (cstate.length != undoredo.length) { - for (int i = 0; i < seq.length; i++) - { - alignment.getHiddenSequences().hideSequence(seq[i]); - } - hasHiddenRows = true; - firePropertyChange("alignment", null, alignment.getSequences()); + return true; } - } - public void showSequence(int index) - { - Vector tmp = alignment.getHiddenSequences().showSequence(index, - hiddenRepSequences); - if (tmp.size() > 0) + for (int i = 0; i < cstate.length; i++) { - if (selectionGroup == null) - { - selectionGroup = new SequenceGroup(); - selectionGroup.setEndRes(alignment.getWidth() - 1); - } - - for (int t = 0; t < tmp.size(); t++) + if (cstate[i] != undoredo[i]) { - selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false); + return true; } - 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; } + return false; } - public void showAllHiddenColumns() + public boolean getCentreColumnLabels() { - colSel.revealAllHiddenColumns(); - hasHiddenColumns = false; + return centreColumnLabels; } - public void showAllHiddenSeqs() + public void setCentreColumnLabels(boolean centrecolumnlabels) { - if (alignment.getHiddenSequences().getSize() > 0) - { - if (selectionGroup == null) - { - selectionGroup = new SequenceGroup(); - selectionGroup.setEndRes(alignment.getWidth() - 1); - } - Vector tmp = alignment.getHiddenSequences().showAll( - hiddenRepSequences); - for (int t = 0; t < tmp.size(); t++) - { - selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false); - } - firePropertyChange("alignment", null, alignment.getSequences()); - hasHiddenRows = false; - hiddenRepSequences = null; - } + centreColumnLabels = centrecolumnlabels; } - public void invertColumnSelection() + /** + * enable or disable the display of Database Cross References in the sequence + * ID tooltip + */ + public void setShowDbRefs(boolean show) { - colSel.invertColumnSelection(0, alignment.getWidth()); + showdbrefs = show; } - public int adjustForHiddenSeqs(int alignmentIndex) - { - return alignment.getHiddenSequences().adjustForHiddenSeqs( - alignmentIndex); + /** + * + * @return true if Database References are to be displayed on tooltips. + */ + public boolean isShowDbRefs() + { + return showdbrefs; } /** - * This method returns an array of new SequenceI objects derived from the - * whole alignment or just the current selection with start and end points - * adjusted * - * @note if you need references to the actual SequenceI objects in the - * alignment or currently selected then use getSequenceSelection() - * @return selection as new sequenceI objects + * @return true if Non-positional features are to be displayed on tooltips. */ - public SequenceI[] getSelectionAsNewSequence() + public boolean isShowNpFeats() { - SequenceI[] sequences; - - if (selectionGroup == null) - { - sequences = alignment.getSequencesArray(); - AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation(); - for (int i = 0; i < sequences.length; i++) - { - sequences[i] = new Sequence(sequences[i], annots); // construct new - // sequence with - // subset of visible - // annotation - } - } - else - { - sequences = selectionGroup.getSelectionAsNewSequences(alignment); - } + return shownpfeats; + } - return sequences; + /** + * enable or disable the display of Non-Positional sequence features in the + * sequence ID tooltip + * + * @param show + */ + public void setShowNpFeats(boolean show) + { + shownpfeats = show; } /** - * get the currently selected sequence objects or all the sequences in the - * alignment. * - * @return array of references to sequence objects + * @return true if view has hidden rows */ - public SequenceI[] getSequenceSelection() + public boolean hasHiddenRows() { - SequenceI[] sequences; - if (selectionGroup == null) - { - sequences = alignment.getSequencesArray(); - } - else - { - sequences = selectionGroup.getSequencesInOrder(alignment); - } - return sequences; + return hasHiddenRows; } /** - * 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[] + * @return true if view has hidden columns */ - public jalview.datamodel.CigarArray getViewAsCigars( - boolean selectedRegionOnly) + public boolean hasHiddenColumns() { - CigarArray selection = null; - SequenceI[] seqs = null; - int i, iSize; - int start = 0, end = 0; - if (selectedRegionOnly && selectionGroup != null) - { - iSize = selectionGroup.getSize(); - seqs = selectionGroup.getSequencesInOrder(alignment); - start = selectionGroup.getStartRes(); - end = selectionGroup.getEndRes(); // inclusive for start and end in - // SeqCigar constructor - } - else - { - iSize = alignment.getHeight(); - seqs = alignment.getSequencesArray(); - end = alignment.getWidth() - 1; - } - SeqCigar[] selseqs = new SeqCigar[iSize]; - for (i = 0; i < iSize; i++) - { - selseqs[i] = new SeqCigar(seqs[i], start, end); - } - selection = new CigarArray(selseqs); - // now construct the CigarArray operations - if (hasHiddenColumns) - { - Vector regions = colSel.getHiddenColumns(); - int[] region; - int hideStart, hideEnd; - int last = start; - for (int j = 0; last < end & j < regions.size(); j++) - { - region = (int[]) regions.elementAt(j); - hideStart = region[0]; - hideEnd = region[1]; - // edit hidden regions to selection range - if (hideStart < last) - { - if (hideEnd > last) - { - hideStart = last; - } - else - { - continue; - } - } + return hasHiddenColumns; + } - if (hideStart > end) - { - break; - } + /** + * when set, view will scroll to show the highlighted position + */ + public boolean followHighlight = true; - if (hideEnd > end) - { - hideEnd = end; - } + /** + * @return true if view should scroll to show the highlighted region of a + * sequence + * @return + */ + public boolean getFollowHighlight() + { + return followHighlight; + } - if (hideStart > hideEnd) - { - break; - } - /** - * form operations... - */ - if (last < hideStart) - { - selection.addOperation(CigarArray.M, hideStart - last); - } - selection.addOperation(CigarArray.D, 1 + hideEnd - hideStart); - last = hideEnd + 1; - } - // Final match if necessary. - if (last < end) - { - selection.addOperation(CigarArray.M, end - last + 1); - } - } - else - { - selection.addOperation(CigarArray.M, end - start + 1); - } - return selection; + public boolean followSelection = true; + + /** + * @return true if view selection should always follow the selections + * broadcast by other selection sources + */ + public boolean getFollowSelection() + { + return followSelection; + } + + 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 setShowSequenceFeaturesHeight(boolean selected) + { + showSeqFeaturesHeight = selected; + } + + public boolean getShowSequenceFeaturesHeight() + { + return showSeqFeaturesHeight; } /** - * return a compact representation of the current alignment selection to pass - * to an analysis function + * return the alignPanel containing the given viewport. Use this to get the + * components currently handling the given viewport. * - * @param selectedOnly - * boolean true to just return the selected view - * @return AlignmentView + * @param av + * @return null or an alignPanel guaranteed to have non-null alignFrame + * reference */ - jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly) + public AlignmentPanel getAlignPanel() { - // 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) + AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(this + .getSequenceSetId()); + AlignmentPanel ap = null; + for (int p = 0; aps != null && p < aps.length; p++) { - return new AlignmentView(aligview, - (selectedOnly && selectionGroup != null) ? selectionGroup - .getStartRes() : 0); + if (aps[p].av == this) + { + return aps[p]; + } } return null; } + public boolean getSortByTree() + { + return sortByTree; + } + + public void setSortByTree(boolean sort) + { + sortByTree = sort; + } + /** - * 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. + * 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. * - * @return String[] + * @param sg + * @param wholewidth */ - public String[] getViewAsString(boolean selectedRegionOnly) + public void expandColSelection(SequenceGroup sg, boolean wholewidth) { - String[] selection = null; - SequenceI[] seqs = null; - int i, iSize; - int start = 0, end = 0; - if (selectedRegionOnly && selectionGroup != null) - { - iSize = selectionGroup.getSize(); - seqs = selectionGroup.getSequencesInOrder(alignment); - start = selectionGroup.getStartRes(); - end = selectionGroup.getEndRes() + 1; - } - else - { - iSize = alignment.getHeight(); - seqs = alignment.getSequencesArray(); - end = alignment.getWidth(); - } - - selection = new String[iSize]; - if (hasHiddenColumns) + int sgs, sge; + if (sg != null + && (sgs = sg.getStartRes()) >= 0 + && sg.getStartRes() <= (sge = sg.getEndRes()) + && (colSel == null || colSel.getSelected() == null || colSel + .getSelected().size() == 0)) { - selection = colSel.getVisibleSequenceStrings(start, end, seqs); - } - else - { - for (i = 0; i < iSize; i++) + if (!wholewidth && alignment.getWidth() == (1 + sge - sgs)) { - selection[i] = seqs[i].getSequenceAsString(start, end); + // do nothing + return; + } + if (colSel == null) + { + colSel = new ColumnSelection(); + } + for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++) + { + colSel.addElement(cspos); } - } - return selection; } - public int[][] getVisibleRegionBoundaries(int min, int max) + public StructureSelectionManager getStructureSelectionManager() { - Vector regions = new Vector(); - int start = min; - int end = max; + return StructureSelectionManager + .getStructureSelectionManager(Desktop.instance); + } - do + /** + * + * @param pdbEntries + * @return a series of SequenceI arrays, one for each PDBEntry, listing which + * sequence in the alignment holds a reference to it + */ + public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries) + { + ArrayList seqvectors = new ArrayList(); + for (PDBEntry pdb : pdbEntries) { - if (hasHiddenColumns) + ArrayList seqs = new ArrayList(); + for (int i = 0; i < alignment.getHeight(); i++) { - if (start == 0) - { - start = colSel.adjustForHiddenColumns(start); - } - - end = colSel.getHiddenBoundaryRight(start); - if (start == end) + Vector pdbs = alignment.getSequenceAt(i).getDatasetSequence() + .getPDBId(); + if (pdbs == null) { - end = max; + continue; } - if (end > max) + SequenceI sq; + for (int p = 0; p < pdbs.size(); p++) { - end = max; - } - } - - regions.addElement(new int[] - { start, end }); + PDBEntry p1 = (PDBEntry) pdbs.elementAt(p); + if (p1.getId().equals(pdb.getId())) + { + if (!seqs.contains(sq = alignment.getSequenceAt(i))) + { + seqs.add(sq); + } - if (hasHiddenColumns) - { - start = colSel.adjustForHiddenColumns(end); - start = colSel.getHiddenBoundaryLeft(start) + 1; + continue; + } + } } - } while (end < max); - - int[][] startEnd = new int[regions.size()][2]; - - regions.copyInto(startEnd); - - return startEnd; - + seqvectors.add(seqs.toArray(new SequenceI[seqs.size()])); + } + return seqvectors.toArray(new SequenceI[seqvectors.size()][]); } - public boolean getShowHiddenMarkers() + public boolean isNormaliseSequenceLogo() { - return showHiddenMarkers; + return normaliseSequenceLogo; } - public void setShowHiddenMarkers(boolean show) + public void setNormaliseSequenceLogo(boolean state) { - showHiddenMarkers = show; + normaliseSequenceLogo = state; } - public String getSequenceSetId() + /** + * + * @return true if alignment characters should be displayed + */ + public boolean isValidCharWidth() { - if (sequenceSetID == null) - { - sequenceSetID = alignment.hashCode() + ""; - } - - return sequenceSetID; + return validCharWidth; } - public void alignmentChanged(AlignmentPanel ap) - { - if (padGaps) - { - alignment.padGaps(); - } + private Hashtable calcIdParams = new Hashtable(); - if (hconsensus != null && autoCalculateConsensus) - { - updateConsensus(ap); - updateConservation(ap); - } + private boolean showAutocalculatedAbove; - // Reset endRes of groups if beyond alignment width - int alWidth = alignment.getWidth(); - Vector groups = alignment.getGroups(); - if (groups != null) - { - for (int i = 0; i < groups.size(); i++) - { - SequenceGroup sg = (SequenceGroup) groups.elementAt(i); - if (sg.getEndRes() > alWidth) - { - sg.setEndRes(alWidth - 1); - } - } - } + public AutoCalcSetting getCalcIdSettingsFor(String calcId) + { + return calcIdParams.get(calcId); + } - if (selectionGroup != null && selectionGroup.getEndRes() > alWidth) + 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) { - selectionGroup.setEndRes(alWidth - 1); + Cache.log.debug("trigger update for " + calcId); } + } - resetAllColourSchemes(); - - // alignment.adjustSequenceAnnotations(); + protected SequenceAnnotationOrder getSortAnnotationsBy() + { + return sortAnnotationsBy; } - void resetAllColourSchemes() + protected void setSortAnnotationsBy(SequenceAnnotationOrder sortAnnotationsBy) { - ColourSchemeI cs = globalColourScheme; - if (cs != null) - { - if (cs instanceof ClustalxColourScheme) - { - ((ClustalxColourScheme) cs).resetClustalX(alignment.getSequences(), - alignment.getWidth()); - } + this.sortAnnotationsBy = sortAnnotationsBy; + } - 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); - } - } + protected boolean isShowAutocalculatedAbove() + { + return showAutocalculatedAbove; + } - int s, sSize = alignment.getGroups().size(); - for (s = 0; s < sSize; s++) - { - SequenceGroup sg = (SequenceGroup) alignment.getGroups().elementAt(s); - if (sg.cs != null && sg.cs instanceof ClustalxColourScheme) - { - ((ClustalxColourScheme) sg.cs).resetClustalX(sg - .getSequences(hiddenRepSequences), sg.getWidth()); - } - sg.recalcConservation(); - } + protected void setShowAutocalculatedAbove(boolean showAutocalculatedAbove) + { + this.showAutocalculatedAbove = showAutocalculatedAbove; } - public Color getSequenceColour(SequenceI seq) + /** + * 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) { - if (sequenceColours == null || !sequenceColours.containsKey(seq)) + /* + * ...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) { - return Color.white; + // ok to continue; } else { - return (Color) sequenceColours.get(seq); + return; } - } - public void setSequenceColour(SequenceI seq, Color col) - { - if (sequenceColours == null) + CommandI mappedCommand = ssm.mapCommand(command, undo, getAlignment(), + getGapCharacter()); + if (mappedCommand != null) { - sequenceColours = new Hashtable(); + AlignmentI[] views = getAlignPanel().alignFrame.getViewAlignments(); + mappedCommand.doCommand(views); + getAlignPanel().alignmentChanged(); } + } - if (col == null) - { - sequenceColours.remove(seq); - } - else - { - sequenceColours.put(seq, col); - } + @Override + public VamsasSource getVamsasSource() + { + return this; } /** - * returns the visible column regions of the alignment + * Add one command to the command history list. * - * @param selectedRegionOnly - * true to just return the contigs intersecting with the - * selected area - * @return + * @param command */ - public int[] getViewAsVisibleContigs(boolean selectedRegionOnly) + public void addToHistoryList(CommandI command) { - int[] viscontigs = null; - int start = 0, end = 0; - if (selectedRegionOnly && selectionGroup != null) + if (this.historyList != null) { - start = selectionGroup.getStartRes(); - end = selectionGroup.getEndRes() + 1; + this.historyList.push(command); + broadcastCommand(command, false); } - 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() + protected void broadcastCommand(CommandI command, boolean undo) { - if (historyList == null || redoList == null) - return new long[] - { -1, -1 }; - return new long[] - { historyList.hashCode(), this.redoList.hashCode() }; + getStructureSelectionManager().commandPerformed(command, undo, getVamsasSource()); } /** - * test if a particular set of hashcodes are different to the hashcodes for - * the undo and redo list. + * Add one command to the command 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 + * @param command */ - public boolean isUndoRedoHashModified(long[] undoredo) + public void addToRedoList(CommandI command) { - if (undoredo == null) + if (this.redoList != null) { - return true; - } - long[] cstate = getUndoRedoHash(); - if (cstate.length != undoredo.length) - { - return true; + this.redoList.push(command); } + broadcastCommand(command, true); + } - for (int i = 0; i < cstate.length; i++) + /** + * Clear the command redo list. + */ + public void clearRedoList() + { + if (this.redoList != null) { - if (cstate[i] != undoredo[i]) - { - return true; - } + this.redoList.clear(); } - return false; } - public boolean getCentreColumnLabels() + public void setHistoryList(Deque list) { - return centreColumnLabels; + this.historyList = list; } - public void setCentreColumnLabels(boolean centrecolumnlabels) + public Deque getHistoryList() { - centreColumnLabels = centrecolumnlabels; + return this.historyList; } - public void updateSequenceIdColours() + public void setRedoList(Deque list) { - Vector groups = alignment.getGroups(); - if (sequenceColours == null) - { - sequenceColours = new Hashtable(); - } - for (int ig = 0, igSize = groups.size(); ig < igSize; ig++) - { - SequenceGroup sg = (SequenceGroup) groups.elementAt(ig); - if (sg.idColour != null) - { - Vector sqs = sg.getSequences(hiddenRepSequences); - for (int s = 0, sSize = sqs.size(); s < sSize; s++) - { - sequenceColours.put(sqs.elementAt(s), sg.idColour); - } - } - } + this.redoList = list; } - /** - * enable or disable the display of Database Cross References in the sequence ID tooltip - */ - public void setShowDbRefs(boolean show) + public Deque getRedoList() { - showdbrefs=show; + return this.redoList; } /** + * 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. * - * @return true if Database References are to be displayed on tooltips. + * @param al + * @param title */ - public boolean isShowDbRefs() + public void addAlignment(AlignmentI al, String title) { - return showdbrefs; + // TODO: promote to AlignViewportI? applet CutAndPasteTransfer is different + + // refactored from FileLoader / CutAndPasteTransfer / SequenceFetcher with + // this comment: + // TODO: create undo object for this JAL-1101 + + /* + * 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()) + { + final Set sequenceNames = getAlignment().getSequenceNames(); + sequenceNames.retainAll(al.getSequenceNames()); + if (!sequenceNames.isEmpty()) // at least one sequence name in both + { + if (openLinkedAlignment(al, title)) + { + return; + } + } + } + + for (int i = 0; i < al.getHeight(); i++) + { + getAlignment().addSequence(al.getSequenceAt(i)); + } + // TODO this call was done by SequenceFetcher but not FileLoader or + // CutAndPasteTransfer. Is it needed? + setEndSeq(getAlignment().getHeight()); + firePropertyChange("alignment", null, getAlignment().getSequences()); } /** + * 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. * - * @return true if Non-positional features are to be displayed on tooltips. - */ - public boolean isShowNpFeats() - { - return shownpfeats; - } - /** - * enable or disable the display of Non-Positional sequence features in the sequence ID tooltip - * @param show + * @param title */ - public void setShowNpFeats(boolean show) + protected boolean openLinkedAlignment(AlignmentI al, String title) { - shownpfeats=show; + 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]); + + if (response != 1 && response != 2) + { + return false; + } + 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) + { + Desktop.addInternalFrame(newAlignFrame, title, + AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT); + } + + /* + * 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) + { + + /* + * Register the mappings (held on the protein alignment) with the + * StructureSelectionManager (for mouseover linking). + */ + ssm.addMappings(protein.getCodonFrames()); + } + else + { + + /* + * 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); + } + + try + { + newAlignFrame.setMaximum(jalview.bin.Cache.getDefault( + "SHOW_FULLSCREEN", + false)); + } catch (java.beans.PropertyVetoException ex) + { + } + + if (openSplitPane) + { + /* + * 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; } }