X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=2cfc1e6d3893a5a1c53b846610cda83b322f08ef;hb=1ae9824ef37ce4ed36d1da986003474b47d1ab11;hp=67db6fcc48c096a8b53fb4511661bcaf04434cf7;hpb=dd81a4ab9d1ffc6168e7a041c7d488db37298cce;p=jalview.git diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java index 67db6fc..2cfc1e6 100644 --- a/src/jalview/viewmodel/AlignmentViewport.java +++ b/src/jalview/viewmodel/AlignmentViewport.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -26,6 +26,8 @@ import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; import jalview.api.FeaturesDisplayedI; import jalview.api.ViewStyleI; +import jalview.commands.CommandI; +import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentView; @@ -40,18 +42,25 @@ import jalview.schemes.Blosum62ColourScheme; import jalview.schemes.ColourSchemeI; import jalview.schemes.PIDColourScheme; import jalview.schemes.ResidueProperties; +import jalview.structure.CommandListener; +import jalview.structure.StructureSelectionManager; +import jalview.structure.VamsasSource; import jalview.viewmodel.styles.ViewStyle; import jalview.workers.AlignCalcManager; +import jalview.workers.ComplementConsensusThread; import jalview.workers.ConsensusThread; import jalview.workers.StrucConsensusThread; import java.awt.Color; +import java.util.ArrayDeque; import java.util.ArrayList; import java.util.BitSet; +import java.util.Deque; import java.util.HashMap; import java.util.Hashtable; import java.util.List; import java.util.Map; +import java.util.Set; /** * base class holding visualization and analysis attributes and common logic for @@ -61,7 +70,7 @@ import java.util.Map; * */ public abstract class AlignmentViewport implements AlignViewportI, - ViewStyleI + ViewStyleI, CommandListener, VamsasSource { protected ViewStyleI viewStyle = new ViewStyle(); @@ -71,6 +80,12 @@ public abstract class AlignmentViewport implements AlignViewportI, */ AlignViewportI codingComplement = null; + FeaturesDisplayedI featuresDisplayed = null; + + protected Deque historyList = new ArrayDeque(); + + protected Deque redoList = new ArrayDeque(); + /** * @param name * @see jalview.api.ViewStyleI#setFontName(java.lang.String) @@ -630,6 +645,8 @@ public abstract class AlignmentViewport implements AlignViewportI, protected AlignmentAnnotation consensus; + protected AlignmentAnnotation complementConsensus; + protected AlignmentAnnotation strucConsensus; protected AlignmentAnnotation conservation; @@ -646,6 +663,11 @@ public abstract class AlignmentViewport implements AlignViewportI, protected Hashtable[] hconsensus = null; /** + * results of cDNA complement consensus visible portion of view + */ + protected Hashtable[] hcomplementConsensus = null; + + /** * results of secondary structure base pair consensus for visible portion of * view */ @@ -675,7 +697,12 @@ public abstract class AlignmentViewport implements AlignViewportI, public void setSequenceConsensusHash(Hashtable[] hconsensus) { this.hconsensus = hconsensus; + } + @Override + public void setComplementConsensusHash(Hashtable[] hconsensus) + { + this.hcomplementConsensus = hconsensus; } @Override @@ -685,6 +712,12 @@ public abstract class AlignmentViewport implements AlignViewportI, } @Override + public Hashtable[] getComplementConsensusHash() + { + return hcomplementConsensus; + } + + @Override public Hashtable[] getRnaStructureConsensusHash() { return hStrucConsensus; @@ -716,6 +749,12 @@ public abstract class AlignmentViewport implements AlignViewportI, } @Override + public AlignmentAnnotation getComplementConsensusAnnotation() + { + return complementConsensus; + } + + @Override public AlignmentAnnotation getAlignmentStrucConsensusAnnotation() { return strucConsensus; @@ -756,6 +795,20 @@ public abstract class AlignmentViewport implements AlignViewportI, { calculator.registerWorker(new ConsensusThread(this, ap)); } + + /* + * A separate thread to compute cDNA consensus for a protein alignment + */ + final AlignmentI al = this.getAlignment(); + if (!al.isNucleotide() && al.getCodonFrames() != null + && !al.getCodonFrames().isEmpty()) + { + if (calculator + .getRegisteredWorkersOfClass(ComplementConsensusThread.class) == null) + { + calculator.registerWorker(new ComplementConsensusThread(this, ap)); + } + } } // --------START Structure Conservation @@ -860,6 +913,7 @@ public abstract class AlignmentViewport implements AlignViewportI, // annotation update method from alignframe to viewport this.showSequenceLogo = showSequenceLogo; calculator.updateAnnotationFor(ConsensusThread.class); + calculator.updateAnnotationFor(ComplementConsensusThread.class); calculator.updateAnnotationFor(StrucConsensusThread.class); } this.showSequenceLogo = showSequenceLogo; @@ -1042,6 +1096,7 @@ public abstract class AlignmentViewport implements AlignViewportI, */ protected String viewId = null; + @Override public String getViewId() { if (viewId == null) @@ -1391,10 +1446,8 @@ public abstract class AlignmentViewport implements AlignViewportI, 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 + // construct new sequence with subset of visible annotation + sequences[i] = new Sequence(sequences[i], annots); } } else @@ -1661,21 +1714,42 @@ public abstract class AlignmentViewport implements AlignViewportI, { initRNAStructure(); } - initConsensus(); + consensus = new AlignmentAnnotation("Consensus", "PID", + new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); + initConsensus(consensus); + + initComplementConsensus(); } } - private void initConsensus() + /** + * If this is a protein alignment and there are mappings to cDNA, add the cDNA + * consensus annotation. + */ + protected void initComplementConsensus() { + if (!alignment.isNucleotide()) + { + final Set codonMappings = alignment + .getCodonFrames(); + if (codonMappings != null && !codonMappings.isEmpty()) + { + complementConsensus = new AlignmentAnnotation("cDNA Consensus", + "PID for cDNA", new Annotation[1], 0f, 100f, + AlignmentAnnotation.BAR_GRAPH); + initConsensus(complementConsensus); + } + } + } - consensus = new AlignmentAnnotation("Consensus", "PID", - new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); - consensus.hasText = true; - consensus.autoCalculated = true; + private void initConsensus(AlignmentAnnotation aa) + { + aa.hasText = true; + aa.autoCalculated = true; if (showConsensus) { - alignment.addAnnotation(consensus); + alignment.addAnnotation(aa); } } @@ -1737,57 +1811,57 @@ public abstract class AlignmentViewport implements AlignViewportI, public int calcPanelHeight() { // setHeight of panels - AlignmentAnnotation[] aa = getAlignment().getAlignmentAnnotation(); + AlignmentAnnotation[] anns = getAlignment().getAlignmentAnnotation(); int height = 0; int charHeight = getCharHeight(); - if (aa != null) + if (anns != null) { BitSet graphgrp = new BitSet(); - for (int i = 0; i < aa.length; i++) + for (AlignmentAnnotation aa : anns) { - if (aa[i] == null) + if (aa == null) { System.err.println("Null annotation row: ignoring."); continue; } - if (!aa[i].visible) + if (!aa.visible) { continue; } - if (aa[i].graphGroup > -1) + if (aa.graphGroup > -1) { - if (graphgrp.get(aa[i].graphGroup)) + if (graphgrp.get(aa.graphGroup)) { continue; } else { - graphgrp.set(aa[i].graphGroup); + graphgrp.set(aa.graphGroup); } } - aa[i].height = 0; + aa.height = 0; - if (aa[i].hasText) + if (aa.hasText) { - aa[i].height += charHeight; + aa.height += charHeight; } - if (aa[i].hasIcons) + if (aa.hasIcons) { - aa[i].height += 16; + aa.height += 16; } - if (aa[i].graph > 0) + if (aa.graph > 0) { - aa[i].height += aa[i].graphHeight; + aa.height += aa.graphHeight; } - if (aa[i].height == 0) + if (aa.height == 0) { - aa[i].height = 20; + aa.height = 20; } - height += aa[i].height; + height += aa.height; } } if (height == 0) @@ -1958,8 +2032,6 @@ public abstract class AlignmentViewport implements AlignViewportI, return getAlignment() == null ? false : getAlignment().isNucleotide(); } - FeaturesDisplayedI featuresDisplayed = null; - @Override public FeaturesDisplayedI getFeaturesDisplayed() { @@ -2242,4 +2314,76 @@ public abstract class AlignmentViewport implements AlignViewportI, { viewStyle.setShowNPFeats(shownpfeats); } + + public abstract StructureSelectionManager getStructureSelectionManager(); + + /** + * Add one command to the command history list. + * + * @param command + */ + public void addToHistoryList(CommandI command) + { + if (this.historyList != null) + { + this.historyList.push(command); + broadcastCommand(command, false); + } + } + + protected void broadcastCommand(CommandI command, boolean undo) + { + getStructureSelectionManager().commandPerformed(command, undo, getVamsasSource()); + } + + /** + * Add one command to the command redo list. + * + * @param command + */ + public void addToRedoList(CommandI command) + { + if (this.redoList != null) + { + this.redoList.push(command); + } + broadcastCommand(command, true); + } + + /** + * Clear the command redo list. + */ + public void clearRedoList() + { + if (this.redoList != null) + { + this.redoList.clear(); + } + } + + public void setHistoryList(Deque list) + { + this.historyList = list; + } + + public Deque getHistoryList() + { + return this.historyList; + } + + public void setRedoList(Deque list) + { + this.redoList = list; + } + + public Deque getRedoList() + { + return this.redoList; + } + + @Override + public VamsasSource getVamsasSource() + { + return this; + } }