X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=5a9fa6b044fab2d5c672fa72f00285a5eea8bfaf;hb=10ff37d2cb03f342ddbed679951d3e2fef0a404b;hp=a7389919cb41560646f9a50bc32dcaf6be1dd331;hpb=7c5e7c1c51a48eab1b217a221df82748c35b76b1;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index a738991..5a9fa6b 100644 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -38,13 +38,15 @@ */ package jalview.gui; +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.datamodel.AlignmentAnnotation; +import jalview.commands.CommandI; +import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; -import jalview.datamodel.Annotation; import jalview.datamodel.ColumnSelection; import jalview.datamodel.PDBEntry; import jalview.datamodel.Sequence; @@ -52,9 +54,11 @@ 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; @@ -62,11 +66,16 @@ 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.Stack; +import java.util.Set; import java.util.Vector; +import javax.swing.JInternalFrame; +import javax.swing.JOptionPane; + /** * DOCUMENT ME! * @@ -74,7 +83,7 @@ import java.util.Vector; * @version $Revision: 1.141 $ */ public class AlignViewport extends AlignmentViewport implements - SelectionSource, VamsasSource, AlignViewportI + SelectionSource, VamsasSource, AlignViewportI, CommandListener { int startRes; @@ -140,9 +149,9 @@ public class AlignViewport extends AlignmentViewport implements boolean gatherViewsHere = false; - Stack historyList = new Stack(); + private Deque historyList = new ArrayDeque(); - Stack redoList = new Stack(); + private Deque redoList = new ArrayDeque(); int thresholdTextColour = 0; @@ -337,10 +346,6 @@ public class AlignViewport extends AlignmentViewport implements false); showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false); showConsensus = Cache.getDefault("SHOW_IDENTITY", true); - consensus = new AlignmentAnnotation("Consensus", "PID", - new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); - consensus.hasText = true; - consensus.autoCalculated = true; } initAutoAnnotation(); if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null) @@ -366,10 +371,10 @@ public class AlignViewport extends AlignmentViewport implements sortByTree = Cache.getDefault("SORT_BY_TREE", false); followSelection = Cache.getDefault("FOLLOW_SELECTIONS", true); sortAnnotationsBy = SequenceAnnotationOrder.valueOf(Cache.getDefault( - Cache.SORT_ANNOTATIONS, SequenceAnnotationOrder.NONE.name())); - showAutocalculatedAbove = Cache -.getDefault(Cache.SHOW_AUTOCALC_ABOVE, - false); + Preferences.SORT_ANNOTATIONS, + SequenceAnnotationOrder.NONE.name())); + showAutocalculatedAbove = Cache.getDefault( + Preferences.SHOW_AUTOCALC_ABOVE, false); } /** @@ -1108,6 +1113,9 @@ public class AlignViewport extends AlignmentViewport implements boolean showSeqFeaturesHeight; + /** + * Send the current selection to be broadcast to any selection listeners. + */ public void sendSelection() { jalview.structure.StructureSelectionManager @@ -1298,4 +1306,295 @@ public class AlignViewport extends AlignmentViewport implements { 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) + { + // ok to continue; + } + else + { + return; + } + + CommandI mappedCommand = ssm.mapCommand(command, undo, getAlignment(), + getGapCharacter()); + if (mappedCommand != null) + { + AlignmentI[] views = getAlignPanel().alignFrame.getViewAlignments(); + mappedCommand.doCommand(views); + getAlignPanel().alignmentChanged(); + } + } + + @Override + public VamsasSource getVamsasSource() + { + return this; + } + + /** + * 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; + } + + /** + * Add the sequences from the given alignment to this viewport. Optionally, + * may give the user the option to open a new frame, or split panel, with cDNA + * and protein linked. + * + * @param al + * @param title + */ + public void addAlignment(AlignmentI al, String title) + { + // TODO: promote to AlignViewportI? applet CutAndPasteTransfer is different + + // 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. + * + * @param title + */ + protected boolean openLinkedAlignment(AlignmentI al, String title) + { + String[] options = new String[] + { MessageManager.getString("action.no"), + MessageManager.getString("label.split_window"), + MessageManager.getString("label.new_window"), }; + final String question = JvSwingUtils.wrapTooltip(true, + MessageManager.getString("label.open_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; + } }