X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=8a95015f483fd8650d55fd8f313d6b3ac2836d7c;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=3254005b30f17a416c69f496aec769cd034991ac;hpb=552a68778a21f29fe5a05fd6840f7f3864e544b1;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index 3254005..8a95015 100644 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.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 2.9) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -38,34 +38,46 @@ */ package jalview.gui; +import jalview.analysis.AlignmentUtils; +import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; import jalview.analysis.NJTree; import jalview.api.AlignViewportI; +import jalview.api.AlignmentViewPanel; +import jalview.api.ViewStyleI; import jalview.bin.Cache; -import jalview.datamodel.AlignmentAnnotation; +import jalview.commands.CommandI; +import jalview.datamodel.AlignedCodonFrame; +import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; -import jalview.datamodel.Annotation; import jalview.datamodel.ColumnSelection; import jalview.datamodel.PDBEntry; +import jalview.datamodel.SearchResults; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.schemes.ColourSchemeProperty; import jalview.schemes.UserColourScheme; +import jalview.structure.CommandListener; import jalview.structure.SelectionSource; import jalview.structure.StructureSelectionManager; import jalview.structure.VamsasSource; +import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; import jalview.ws.params.AutoCalcSetting; -import java.awt.Color; import java.awt.Container; +import java.awt.Dimension; import java.awt.Font; import java.awt.Rectangle; import java.util.ArrayList; import java.util.Hashtable; -import java.util.Stack; +import java.util.List; +import java.util.Set; import java.util.Vector; +import javax.swing.JInternalFrame; +import javax.swing.JOptionPane; + /** * DOCUMENT ME! * @@ -73,75 +85,30 @@ import java.util.Vector; * @version $Revision: 1.141 $ */ public class AlignViewport extends AlignmentViewport implements - SelectionSource, VamsasSource, AlignViewportI + SelectionSource, CommandListener { - int startRes; - - int endRes; - - int startSeq; - - int endSeq; - - boolean showJVSuffix = true; - - boolean showText = true; - - boolean showColourText = false; - - boolean showBoxes = true; - - boolean wrapAlignment = false; - - boolean renderGaps = true; - - boolean showSequenceFeatures = false; - - boolean showAnnotation = true; - - int charHeight; - - int charWidth; - - boolean validCharWidth; - - int wrappedWidth; - Font font; - boolean seqNameItalics; - NJTree currentTree = null; - boolean scaleAboveWrapped = false; - - boolean scaleLeftWrapped = true; - - boolean scaleRightWrapped = true; - - boolean showHiddenMarkers = true; - boolean cursorMode = false; boolean antiAlias = false; - Rectangle explodedPosition; + private Rectangle explodedGeometry; String viewName; - boolean gatherViewsHere = false; - - Stack historyList = new Stack(); - - Stack redoList = new Stack(); - - int thresholdTextColour = 0; - - Color textColour = Color.black; - - Color textColour2 = Color.white; + /* + * Flag set true on the view that should 'gather' multiple views of the same + * sequence set id when a project is reloaded. Set false on all views when + * they are 'exploded' into separate windows. Set true on the current view + * when 'Gather' is performed, and also on the first tab when the first new + * view is created. + */ + private boolean gatherViewsHere = false; - boolean rightAlignIds = false; + private AnnotationColumnChooser annotationColumnSelectionState; /** * Creates a new AlignViewport object. @@ -198,16 +165,7 @@ public class AlignViewport extends AlignmentViewport implements setAlignment(al); if (hiddenColumns != null) { - this.colSel = hiddenColumns; - if (hiddenColumns.getHiddenColumns() != null - && hiddenColumns.getHiddenColumns().size() > 0) - { - hasHiddenColumns = true; - } - else - { - hasHiddenColumns = false; - } + colSel = hiddenColumns; } init(); } @@ -254,46 +212,55 @@ public class AlignViewport extends AlignmentViewport implements setAlignment(al); if (hiddenColumns != null) { - this.colSel = hiddenColumns; - if (hiddenColumns.getHiddenColumns() != null - && hiddenColumns.getHiddenColumns().size() > 0) - { - hasHiddenColumns = true; - } - else - { - hasHiddenColumns = false; - } + colSel = hiddenColumns; } init(); } - void init() + /** + * Apply any settings saved in user preferences + */ + private void applyViewProperties() { - this.startRes = 0; - this.endRes = alignment.getWidth() - 1; - this.startSeq = 0; - this.endSeq = alignment.getHeight() - 1; - antiAlias = Cache.getDefault("ANTI_ALIAS", false); - showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true); - showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true); + viewStyle.setShowJVSuffix(Cache.getDefault("SHOW_JVSUFFIX", true)); + setShowAnnotation(Cache.getDefault("SHOW_ANNOTATIONS", true)); - rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false); - centreColumnLabels = Cache.getDefault("CENTRE_COLUMN_LABELS", false); + setRightAlignIds(Cache.getDefault("RIGHT_ALIGN_IDS", false)); + setCentreColumnLabels(Cache.getDefault("CENTRE_COLUMN_LABELS", false)); autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true); setPadGaps(Cache.getDefault("PAD_GAPS", true)); - shownpfeats = Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true); - showdbrefs = Cache.getDefault("SHOW_DBREFS_TOOLTIP", true); + setShowNPFeats(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true)); + setShowDBRefs(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true)); + viewStyle.setSeqNameItalics(Cache.getDefault("ID_ITALICS", true)); + viewStyle.setWrapAlignment(Cache.getDefault("WRAP_ALIGNMENT", false)); + viewStyle.setShowUnconserved(Cache + .getDefault("SHOW_UNCONSERVED", false)); + sortByTree = Cache.getDefault("SORT_BY_TREE", false); + followSelection = Cache.getDefault("FOLLOW_SELECTIONS", true); + sortAnnotationsBy = SequenceAnnotationOrder.valueOf(Cache.getDefault( + Preferences.SORT_ANNOTATIONS, + SequenceAnnotationOrder.NONE.name())); + showAutocalculatedAbove = Cache.getDefault( + Preferences.SHOW_AUTOCALC_ABOVE, false); + viewStyle.setScaleProteinAsCdna(Cache.getDefault( + Preferences.SCALE_PROTEIN_TO_CDNA, true)); + } + + void init() + { + this.startRes = 0; + this.endRes = alignment.getWidth() - 1; + this.startSeq = 0; + this.endSeq = alignment.getHeight() - 1; + applyViewProperties(); String fontName = Cache.getDefault("FONT_NAME", "SansSerif"); String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + ""); String fontSize = Cache.getDefault("FONT_SIZE", "10"); - seqNameItalics = Cache.getDefault("ID_ITALICS", true); - int style = 0; if (fontStyle.equals("bold")) @@ -305,7 +272,7 @@ public class AlignViewport extends AlignmentViewport implements style = 2; } - setFont(new Font(fontName, style, Integer.parseInt(fontSize))); + setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true); alignment .setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0)); @@ -328,22 +295,26 @@ 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) + String colourProperty = alignment.isNucleotide() ? Preferences.DEFAULT_COLOUR_NUC + : Preferences.DEFAULT_COLOUR_PROT; + String propertyValue = Cache.getProperty(colourProperty); + if (propertyValue == null) + { + // fall back on this property for backwards compatibility + propertyValue = Cache.getProperty(Preferences.DEFAULT_COLOUR); + } + if (propertyValue != null) { globalColourScheme = ColourSchemeProperty.getColour(alignment, - jalview.bin.Cache.getProperty("DEFAULT_COLOUR")); + propertyValue); if (globalColourScheme instanceof UserColourScheme) { globalColourScheme = UserDefinedColours.loadDefaultColours(); ((UserColourScheme) globalColourScheme).setThreshold(0, - getIgnoreGapsConsensus()); + isIgnoreGapsConsensus()); } if (globalColourScheme != null) @@ -351,44 +322,9 @@ public class AlignViewport extends AlignmentViewport implements globalColourScheme.setConsensus(hconsensus); } } - - wrapAlignment = jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false); - showUnconserved = jalview.bin.Cache.getDefault("SHOW_UNCONSERVED", - false); - sortByTree = jalview.bin.Cache.getDefault("SORT_BY_TREE", false); - followSelection = jalview.bin.Cache.getDefault("FOLLOW_SELECTIONS", - true); - } - - /** - * set the flag - * - * @param b - * features are displayed if true - */ - public void setShowSequenceFeatures(boolean b) - { - showSequenceFeatures = b; - } - - public boolean getShowSequenceFeatures() - { - return showSequenceFeatures; } /** - * centre columnar annotation labels in displayed alignment annotation TODO: - * add to jalviewXML and annotation display settings - */ - boolean centreColumnLabels = false; - - private boolean showdbrefs; - - private boolean shownpfeats; - - // --------END Structure Conservation - - /** * get the consensus sequence as displayed under the PID consensus annotation * row. * @@ -426,24 +362,43 @@ public class AlignViewport extends AlignmentViewport implements return sq; } + boolean validCharWidth; + /** - * DOCUMENT ME! + * update view settings with the given font. You may need to call + * alignPanel.fontChanged to update the layout geometry * - * @return DOCUMENT ME! + * @param setGrid + * when true, charWidth/height is set according to font mentrics */ - public int getStartRes() + public void setFont(Font f, boolean setGrid) { - return startRes; + font = f; + + Container c = new Container(); + + java.awt.FontMetrics fm = c.getFontMetrics(font); + int w = viewStyle.getCharWidth(), ww = fm.charWidth('M'), h = viewStyle + .getCharHeight(); + if (setGrid) + { + setCharHeight(fm.getHeight()); + setCharWidth(ww); + } + viewStyle.setFontName(font.getName()); + viewStyle.setFontStyle(font.getStyle()); + viewStyle.setFontSize(font.getSize()); + + validCharWidth = true; } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getEndRes() + @Override + public void setViewStyle(ViewStyleI settingsForView) { - return endRes; + super.setViewStyle(settingsForView); + setFont(new Font(viewStyle.getFontName(), viewStyle.getFontStyle(), + viewStyle.getFontSize()), false); + } /** @@ -451,75 +406,75 @@ public class AlignViewport extends AlignmentViewport implements * * @return DOCUMENT ME! */ - public int getStartSeq() + public Font getFont() { - return startSeq; + return font; } /** * DOCUMENT ME! * - * @param res + * @param align * DOCUMENT ME! */ - public void setStartRes(int res) + public void setAlignment(AlignmentI align) { - this.startRes = res; + replaceMappings(align); + this.alignment = align; } /** - * DOCUMENT ME! + * Replace any codon mappings for this viewport with those for the given + * viewport * - * @param seq - * DOCUMENT ME! + * @param align */ - public void setStartSeq(int seq) + public void replaceMappings(AlignmentI align) { - this.startSeq = seq; - } - /** - * DOCUMENT ME! - * - * @param res - * DOCUMENT ME! - */ - public void setEndRes(int res) - { - if (res > (alignment.getWidth() - 1)) + /* + * Deregister current mappings (if any) + */ + deregisterMappings(); + + /* + * Register new mappings (if any) + */ + if (align != null) { - // log.System.out.println(" Corrected res from " + res + " to maximum " + - // (alignment.getWidth()-1)); - res = alignment.getWidth() - 1; + StructureSelectionManager ssm = StructureSelectionManager + .getStructureSelectionManager(Desktop.instance); + ssm.registerMappings(align.getCodonFrames()); } - if (res < 0) + /* + * replace mappings on our alignment + */ + if (alignment != null && align != null) { - res = 0; + alignment.setCodonFrames(align.getCodonFrames()); } - - this.endRes = res; } - /** - * DOCUMENT ME! - * - * @param seq - * DOCUMENT ME! - */ - public void setEndSeq(int seq) + protected void deregisterMappings() { - if (seq > alignment.getHeight()) - { - seq = alignment.getHeight(); - } - - if (seq < 0) + AlignmentI al = getAlignment(); + if (al != null) { - seq = 0; + Set mappings = al.getCodonFrames(); + if (mappings != null) + { + StructureSelectionManager ssm = StructureSelectionManager + .getStructureSelectionManager(Desktop.instance); + for (AlignedCodonFrame acf : mappings) + { + if (noReferencesTo(acf)) + { + ssm.deregisterMapping(acf); + } + } + } } - - this.endSeq = seq; } /** @@ -527,27 +482,23 @@ public class AlignViewport extends AlignmentViewport implements * * @return DOCUMENT ME! */ - public int getEndSeq() + public char getGapCharacter() { - return endSeq; + return getAlignment().getGapCharacter(); } /** * DOCUMENT ME! * - * @param f + * @param gap * DOCUMENT ME! */ - public void setFont(Font f) + public void setGapCharacter(char gap) { - font = f; - - Container c = new Container(); - - java.awt.FontMetrics fm = c.getFontMetrics(font); - setCharHeight(fm.getHeight()); - setCharWidth(fm.charWidth('M')); - validCharWidth = true; + if (getAlignment() != null) + { + getAlignment().setGapCharacter(gap); + } } /** @@ -555,20 +506,20 @@ public class AlignViewport extends AlignmentViewport implements * * @return DOCUMENT ME! */ - public Font getFont() + public ColumnSelection getColumnSelection() { - return font; + return colSel; } /** * DOCUMENT ME! * - * @param w + * @param tree * DOCUMENT ME! */ - public void setCharWidth(int w) + public void setCurrentTree(NJTree tree) { - this.charWidth = w; + currentTree = tree; } /** @@ -576,686 +527,584 @@ public class AlignViewport extends AlignmentViewport implements * * @return DOCUMENT ME! */ - public int getCharWidth() + public NJTree getCurrentTree() { - return charWidth; + return currentTree; } /** - * DOCUMENT ME! + * returns the visible column regions of the alignment * - * @param h - * DOCUMENT ME! + * @param selectedRegionOnly + * true to just return the contigs intersecting with the selected + * area + * @return */ - public void setCharHeight(int h) + public int[] getViewAsVisibleContigs(boolean selectedRegionOnly) { - this.charHeight = h; + 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; } /** - * DOCUMENT ME! + * get hash of undo and redo list for the alignment * - * @return DOCUMENT ME! + * @return long[] { historyList.hashCode, redoList.hashCode }; */ - public int getCharHeight() + public long[] getUndoRedoHash() { - return charHeight; + // TODO: JAL-1126 + if (historyList == null || redoList == null) + { + return new long[] { -1, -1 }; + } + return new long[] { historyList.hashCode(), this.redoList.hashCode() }; } /** - * DOCUMENT ME! + * test if a particular set of hashcodes are different to the hashcodes for + * the undo and redo list. * - * @param w - * DOCUMENT ME! + * @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 void setWrappedWidth(int w) + public boolean isUndoRedoHashModified(long[] undoredo) { - this.wrappedWidth = w; + if (undoredo == null) + { + return true; + } + long[] cstate = getUndoRedoHash(); + if (cstate.length != undoredo.length) + { + return true; + } + + for (int i = 0; i < cstate.length; i++) + { + if (cstate[i] != undoredo[i]) + { + return true; + } + } + return false; } + public boolean followSelection = true; + /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! + * @return true if view selection should always follow the selections + * broadcast by other selection sources */ - public int getWrappedWidth() + public boolean getFollowSelection() { - return wrappedWidth; + return followSelection; } /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! + * Send the current selection to be broadcast to any selection listeners. */ - public AlignmentI getAlignment() + public void sendSelection() { - return alignment; + jalview.structure.StructureSelectionManager + .getStructureSelectionManager(Desktop.instance).sendSelection( + new SequenceGroup(getSelectionGroup()), + new ColumnSelection(getColumnSelection()), this); } /** - * DOCUMENT ME! + * return the alignPanel containing the given viewport. Use this to get the + * components currently handling the given viewport. * - * @param align - * DOCUMENT ME! + * @param av + * @return null or an alignPanel guaranteed to have non-null alignFrame + * reference */ - public void setAlignment(AlignmentI align) + public AlignmentPanel getAlignPanel() { - if (alignment != null && alignment.getCodonFrames() != null) - { - StructureSelectionManager.getStructureSelectionManager( - Desktop.instance).removeMappings(alignment.getCodonFrames()); - } - this.alignment = align; - if (alignment != null && alignment.getCodonFrames() != null) + AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(this + .getSequenceSetId()); + for (int p = 0; aps != null && p < aps.length; p++) { - StructureSelectionManager.getStructureSelectionManager( - Desktop.instance).addMappings(alignment.getCodonFrames()); + if (aps[p].av == this) + { + return aps[p]; + } } + return null; } - /** - * DOCUMENT ME! - * - * @param state - * DOCUMENT ME! - */ - public void setWrapAlignment(boolean state) + public boolean getSortByTree() { - wrapAlignment = state; + return sortByTree; } - /** - * DOCUMENT ME! - * - * @param state - * DOCUMENT ME! - */ - public void setShowText(boolean state) + public void setSortByTree(boolean sort) { - showText = state; + sortByTree = sort; } /** - * DOCUMENT ME! - * - * @param state - * DOCUMENT ME! - */ - public void setRenderGaps(boolean state) - { - renderGaps = state; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getColourText() - { - return showColourText; - } - - /** - * DOCUMENT ME! - * - * @param state - * DOCUMENT ME! - */ - public void setColourText(boolean state) - { - showColourText = state; - } - - /** - * DOCUMENT ME! - * - * @param state - * DOCUMENT ME! - */ - public void setShowBoxes(boolean state) - { - showBoxes = state; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getWrapAlignment() - { - return wrapAlignment; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getShowText() - { - return showText; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getShowBoxes() - { - return showBoxes; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public char getGapCharacter() - { - return getAlignment().getGapCharacter(); - } - - /** - * DOCUMENT ME! + * 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 gap - * DOCUMENT ME! + * @param sg + * @param wholewidth */ - public void setGapCharacter(char gap) + public void expandColSelection(SequenceGroup sg, boolean wholewidth) { - if (getAlignment() != null) + int sgs, sge; + if (sg != null + && (sgs = sg.getStartRes()) >= 0 + && sg.getStartRes() <= (sge = sg.getEndRes()) + && (colSel == null || colSel.getSelected() == null || colSel + .getSelected().size() == 0)) { - getAlignment().setGapCharacter(gap); + if (!wholewidth && alignment.getWidth() == (1 + sge - sgs)) + { + // do nothing + return; + } + if (colSel == null) + { + colSel = new ColumnSelection(); + } + for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++) + { + colSel.addElement(cspos); + } } } /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! + * Returns the (Desktop) instance of the StructureSelectionManager */ - public ColumnSelection getColumnSelection() + @Override + public StructureSelectionManager getStructureSelectionManager() { - return colSel; + return StructureSelectionManager + .getStructureSelectionManager(Desktop.instance); } /** - * DOCUMENT ME! * - * @param tree - * DOCUMENT ME! + * @param pdbEntries + * @return an array of SequenceI arrays, one for each PDBEntry, listing which + * sequences in the alignment hold a reference to it */ - public void setCurrentTree(NJTree tree) + public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries) { - currentTree = tree; + List seqvectors = new ArrayList(); + for (PDBEntry pdb : pdbEntries) + { + List seqs = new ArrayList(); + for (SequenceI sq : alignment.getSequences()) + { + Vector pdbs = sq.getDatasetSequence().getAllPDBEntries(); + if (pdbs == null) + { + continue; + } + for (PDBEntry p1 : pdbs) + { + if (p1.getId().equals(pdb.getId())) + { + if (!seqs.contains(sq)) + { + seqs.add(sq); + continue; + } + } + } + } + seqvectors.add(seqs.toArray(new SequenceI[seqs.size()])); + } + return seqvectors.toArray(new SequenceI[seqvectors.size()][]); } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public NJTree getCurrentTree() + public boolean isNormaliseSequenceLogo() { - return currentTree; + return normaliseSequenceLogo; } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getShowJVSuffix() + public void setNormaliseSequenceLogo(boolean state) { - return showJVSuffix; + normaliseSequenceLogo = state; } /** - * DOCUMENT ME! * - * @param b - * DOCUMENT ME! + * @return true if alignment characters should be displayed */ - public void setShowJVSuffix(boolean b) + public boolean isValidCharWidth() { - showJVSuffix = b; + return validCharWidth; } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getShowAnnotation() - { - return showAnnotation; - } + private Hashtable calcIdParams = new Hashtable(); - /** - * DOCUMENT ME! - * - * @param b - * DOCUMENT ME! - */ - public void setShowAnnotation(boolean b) + public AutoCalcSetting getCalcIdSettingsFor(String calcId) { - showAnnotation = b; + return calcIdParams.get(calcId); } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getScaleAboveWrapped() + public void setCalcIdSettingsFor(String calcId, AutoCalcSetting settings, + boolean needsUpdate) { - return scaleAboveWrapped; + calcIdParams.put(calcId, settings); + // TODO: create a restart list to trigger any calculations that need to be + // restarted after load + // calculator.getRegisteredWorkersOfClass(settings.getWorkerClass()) + if (needsUpdate) + { + Cache.log.debug("trigger update for " + calcId); + } } /** - * DOCUMENT ME! + * 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
    • + *
* - * @return DOCUMENT ME! - */ - public boolean getScaleLeftWrapped() - { - return scaleLeftWrapped; - } + * @param command + * @param undo + * @param ssm + */ + @Override + public void mirrorCommand(CommandI command, boolean undo, + StructureSelectionManager ssm, VamsasSource source) + { + /* + * Do nothing unless we are a 'complement' of the source. May replace this + * with direct calls not via SSM. + */ + if (source instanceof AlignViewportI + && ((AlignViewportI) source).getCodingComplement() == this) + { + // ok to continue; + } + else + { + return; + } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getScaleRightWrapped() - { - return scaleRightWrapped; + CommandI mappedCommand = ssm.mapCommand(command, undo, getAlignment(), + getGapCharacter()); + if (mappedCommand != null) + { + AlignmentI[] views = getAlignPanel().alignFrame.getViewAlignments(); + mappedCommand.doCommand(views); + getAlignPanel().alignmentChanged(); + } } /** - * DOCUMENT ME! + * 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 b - * DOCUMENT ME! + * @param al + * @param title */ - public void setScaleAboveWrapped(boolean b) + public void addAlignment(AlignmentI al, String title) { - scaleAboveWrapped = b; - } + // TODO: promote to AlignViewportI? applet CutAndPasteTransfer is different - /** - * DOCUMENT ME! - * - * @param b - * DOCUMENT ME! - */ - public void setScaleLeftWrapped(boolean b) - { - scaleLeftWrapped = b; - } + // JBPComment: title is a largely redundant parameter at the moment + // JBPComment: this really should be an 'insert/pre/append' controller + // JBPComment: but the DNA/Protein check makes it a bit more complex - /** - * DOCUMENT ME! - * - * @param b - * DOCUMENT ME! - */ - public void setScaleRightWrapped(boolean b) - { - scaleRightWrapped = b; - } + // refactored from FileLoader / CutAndPasteTransfer / SequenceFetcher with + // this comment: + // TODO: create undo object for this JAL-1101 - public void setDataset(boolean b) - { - isDataset = b; - } + /* + * If any cDNA/protein mappings can be made between the alignments, offer to + * open a linked alignment with split frame option. + */ + if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true)) + { + if (al.getDataset() == null) + { + // need to create ds seqs + for (SequenceI sq : al.getSequences()) + { + if (sq.getDatasetSequence() == null) + { + sq.createDatasetSequence(); + } + } + } + if (AlignmentUtils.isMappable(al, getAlignment())) + { + if (openLinkedAlignment(al, title)) + { + return; + } + } + } - public boolean isDataset() - { - return isDataset; - } + /* + * No mappings, or offer declined - add sequences to this alignment + */ + // TODO: JAL-407 regardless of above - identical sequences (based on ID and + // provenance) should share the same dataset sequence - public boolean getShowHiddenMarkers() - { - return showHiddenMarkers; - } + for (int i = 0; i < al.getHeight(); i++) + { + getAlignment().addSequence(al.getSequenceAt(i)); + } - public void setShowHiddenMarkers(boolean show) - { - showHiddenMarkers = show; + setEndSeq(getAlignment().getHeight()); + firePropertyChange("alignment", null, getAlignment().getSequences()); } /** - * returns the visible column regions of the alignment + * Show a dialog with the option to open and link (cDNA <-> protein) as a new + * alignment, either as a standalone alignment or in a split frame. Returns + * true if the new alignment was opened, false if not, because the user + * declined the offer. * - * @param selectedRegionOnly - * true to just return the contigs intersecting with the selected - * area - * @return - */ - public int[] getViewAsVisibleContigs(boolean selectedRegionOnly) - { - int[] viscontigs = null; - int start = 0, end = 0; - if (selectedRegionOnly && selectionGroup != null) + * @param al + * @param title + */ + protected boolean openLinkedAlignment(AlignmentI al, String title) + { + String[] options = new String[] { + MessageManager.getString("action.no"), + MessageManager.getString("label.split_window"), + MessageManager.getString("label.new_window"), }; + final String question = JvSwingUtils.wrapTooltip(true, + MessageManager.getString("label.open_split_window?")); + int response = JOptionPane.showOptionDialog(Desktop.desktop, question, + MessageManager.getString("label.open_split_window"), + JOptionPane.DEFAULT_OPTION, JOptionPane.PLAIN_MESSAGE, null, + options, options[0]); + + if (response != 1 && response != 2) { - start = selectionGroup.getStartRes(); - end = selectionGroup.getEndRes() + 1; + return false; } - else + final boolean openSplitPane = (response == 1); + final boolean openInNewWindow = (response == 2); + + /* + * 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(); + AlignmentI protein = al.isNucleotide() ? thisAlignment : al; + final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment; + + /* + * Map sequences. At least one should get mapped as we have already passed + * the test for 'mappability'. Any mappings made will be added to the + * protein alignment. Note creating dataset sequences on the new alignment + * is a pre-requisite for building mappings. + */ + al.setDataset(null); + AlignmentUtils.mapProteinToCdna(protein, cdna); + + /* + * Create the AlignFrame for the added alignment. If it is protein, mappings + * are registered with StructureSelectionManager as a side-effect. + */ + AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT); + newAlignFrame.setTitle(title); + 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) { - end = alignment.getWidth(); + Desktop.addInternalFrame(newAlignFrame, title, + AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); } - viscontigs = colSel.getVisibleContigs(start, end); - return viscontigs; - } - - /** - * get hash of undo and redo list for the alignment - * - * @return long[] { historyList.hashCode, redoList.hashCode }; - */ - public long[] getUndoRedoHash() - { - // TODO: JAL-1126 - if (historyList == null || redoList == null) - return new long[] - { -1, -1 }; - return new long[] - { historyList.hashCode(), this.redoList.hashCode() }; - } - /** - * test if a particular set of hashcodes are different to the hashcodes for - * the undo and redo list. - * - * @param undoredo - * the stored set of hashcodes as returned by getUndoRedoHash - * @return true if the hashcodes differ (ie the alignment has been edited) or - * the stored hashcode array differs in size - */ - public boolean isUndoRedoHashModified(long[] undoredo) - { - if (undoredo == null) + try { - return true; - } - long[] cstate = getUndoRedoHash(); - if (cstate.length != undoredo.length) + newAlignFrame.setMaximum(jalview.bin.Cache.getDefault( + "SHOW_FULLSCREEN", false)); + } catch (java.beans.PropertyVetoException ex) { - return true; } - for (int i = 0; i < cstate.length; i++) + if (openSplitPane) { - if (cstate[i] != undoredo[i]) - { - return true; - } + al.alignAs(thisAlignment); + protein = openSplitFrame(newAlignFrame, thisAlignment); } - return false; - } - - public boolean getCentreColumnLabels() - { - return centreColumnLabels; - } - - public void setCentreColumnLabels(boolean centrecolumnlabels) - { - centreColumnLabels = centrecolumnlabels; - } - /** - * enable or disable the display of Database Cross References in the sequence - * ID tooltip - */ - public void setShowDbRefs(boolean show) - { - showdbrefs = show; + return true; } /** + * Helper method to open a new SplitFrame holding linked dna and protein + * alignments. * - * @return true if Database References are to be displayed on tooltips. + * @param newAlignFrame + * containing a new alignment to be shown + * @param complement + * cdna/protein complement alignment to show in the other split half + * @return the protein alignment in the split frame */ - public boolean isShowDbRefs() + protected AlignmentI openSplitFrame(AlignFrame newAlignFrame, + AlignmentI complement) { - return showdbrefs; - } + /* + * Make a new frame with a copy of the alignment we are adding to. If this + * is protein, the mappings to cDNA will be registered with + * StructureSelectionManager as a side-effect. + */ + AlignFrame copyMe = new AlignFrame(complement, + AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); + copyMe.setTitle(getAlignPanel().alignFrame.getTitle()); - /** - * - * @return true if Non-positional features are to be displayed on tooltips. - */ - public boolean isShowNpFeats() - { - return shownpfeats; - } + AlignmentI al = newAlignFrame.viewport.getAlignment(); + final AlignFrame proteinFrame = al.isNucleotide() ? copyMe + : newAlignFrame; + final AlignFrame cdnaFrame = al.isNucleotide() ? newAlignFrame : copyMe; + cdnaFrame.setVisible(true); + proteinFrame.setVisible(true); + String linkedTitle = MessageManager + .getString("label.linked_view_title"); - /** - * enable or disable the display of Non-Positional sequence features in the - * sequence ID tooltip - * - * @param show - */ - public void setShowNpFeats(boolean show) - { - shownpfeats = show; + /* + * Open in split pane. DNA sequence above, protein below. + */ + JInternalFrame splitFrame = new SplitFrame(cdnaFrame, proteinFrame); + Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1); + + return proteinFrame.viewport.getAlignment(); } - /** - * - * @return true if view has hidden rows - */ - public boolean hasHiddenRows() + public AnnotationColumnChooser getAnnotationColumnSelectionState() { - return hasHiddenRows; + return annotationColumnSelectionState; } - /** - * - * @return true if view has hidden columns - */ - public boolean hasHiddenColumns() + public void setAnnotationColumnSelectionState( + AnnotationColumnChooser currentAnnotationColumnSelectionState) { - return hasHiddenColumns; + this.annotationColumnSelectionState = currentAnnotationColumnSelectionState; } - /** - * when set, view will scroll to show the highlighted position - */ - public boolean followHighlight = true; - - /** - * @return true if view should scroll to show the highlighted region of a - * sequence - * @return - */ - public boolean getFollowHighlight() + @Override + public void setIdWidth(int i) { - return followHighlight; + super.setIdWidth(i); + AlignmentPanel ap = getAlignPanel(); + if (ap != null) + { + // modify GUI elements to reflect geometry change + Dimension idw = getAlignPanel().getIdPanel().getIdCanvas() + .getPreferredSize(); + idw.width = i; + getAlignPanel().getIdPanel().getIdCanvas().setPreferredSize(idw); + } } - public boolean followSelection = true; - - /** - * @return true if view selection should always follow the selections - * broadcast by other selection sources - */ - public boolean getFollowSelection() + public Rectangle getExplodedGeometry() { - return followSelection; + return explodedGeometry; } - boolean showSeqFeaturesHeight; - - public void sendSelection() + public void setExplodedGeometry(Rectangle explodedPosition) { - jalview.structure.StructureSelectionManager - .getStructureSelectionManager(Desktop.instance).sendSelection( - new SequenceGroup(getSelectionGroup()), - new ColumnSelection(getColumnSelection()), this); + this.explodedGeometry = explodedPosition; } - public void setShowSequenceFeaturesHeight(boolean selected) + public boolean isGatherViewsHere() { - showSeqFeaturesHeight = selected; + return gatherViewsHere; } - public boolean getShowSequenceFeaturesHeight() + public void setGatherViewsHere(boolean gatherViewsHere) { - return showSeqFeaturesHeight; + this.gatherViewsHere = gatherViewsHere; } /** - * 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 + * If this viewport has a (Protein/cDNA) complement, then scroll the + * complementary alignment to match this one. */ - public AlignmentPanel getAlignPanel() + public void scrollComplementaryAlignment() { - AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(this - .getSequenceSetId()); - AlignmentPanel ap = null; - for (int p = 0; aps != null && p < aps.length; p++) + /* + * Populate a SearchResults object with the mapped location to scroll to. If + * there is no complement, or it is not following highlights, or no mapping + * is found, the result will be empty. + */ + SearchResults sr = new SearchResults(); + int verticalOffset = findComplementScrollTarget(sr); + if (!sr.isEmpty()) { - if (aps[p].av == this) - { - return aps[p]; - } + // TODO would like next line without cast but needs more refactoring... + final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement()) + .getAlignPanel(); + complementPanel.setFollowingComplementScroll(true); + complementPanel.scrollToCentre(sr, verticalOffset); } - return null; - } - - public boolean getSortByTree() - { - return sortByTree; - } - - public void setSortByTree(boolean sort) - { - sortByTree = sort; } /** - * synthesize a column selection if none exists so it covers the given - * selection group. if wholewidth is false, no column selection is made if the - * selection group covers the whole alignment width. + * Answers true if no alignment holds a reference to the given mapping * - * @param sg - * @param wholewidth + * @param acf + * @return */ - public void expandColSelection(SequenceGroup sg, boolean wholewidth) + protected boolean noReferencesTo(AlignedCodonFrame acf) { - int sgs, sge; - if (sg != null - && (sgs = sg.getStartRes()) >= 0 - && sg.getStartRes() <= (sge = sg.getEndRes()) - && (colSel == null || colSel.getSelected() == null || colSel - .getSelected().size() == 0)) + AlignFrame[] frames = Desktop.getAlignFrames(); + if (frames == null) { - if (!wholewidth && alignment.getWidth() == (1 + sge - sgs)) - { - // do nothing - return; - } - if (colSel == null) - { - colSel = new ColumnSelection(); - } - for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++) - { - colSel.addElement(cspos); - } + return true; } - } - - 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) - { - ArrayList seqvectors = new ArrayList(); - for (PDBEntry pdb : pdbEntries) + for (AlignFrame af : frames) { - ArrayList seqs = new ArrayList(); - for (int i = 0; i < alignment.getHeight(); i++) + if (!af.isClosed()) { - Vector pdbs = alignment.getSequenceAt(i).getDatasetSequence() - .getPDBId(); - if (pdbs == null) - continue; - SequenceI sq; - for (int p = 0; p < pdbs.size(); p++) + for (AlignmentViewPanel ap : af.getAlignPanels()) { - PDBEntry p1 = (PDBEntry) pdbs.elementAt(p); - if (p1.getId().equals(pdb.getId())) + AlignmentI al = ap.getAlignment(); + if (al != null && al.getCodonFrames().contains(acf)) { - if (!seqs.contains(sq = alignment.getSequenceAt(i))) - seqs.add(sq); - - continue; + return false; } } } - seqvectors.add(seqs.toArray(new SequenceI[seqs.size()])); } - return seqvectors.toArray(new SequenceI[seqvectors.size()][]); - } - - public boolean isNormaliseSequenceLogo() - { - return normaliseSequenceLogo; - } - - public void setNormaliseSequenceLogo(boolean state) - { - normaliseSequenceLogo = state; + return true; } - /** - * - * @return true if alignment characters should be displayed - */ - public boolean isValidCharWidth() - { - return validCharWidth; - } - - private Hashtable calcIdParams = new Hashtable(); - - public AutoCalcSetting getCalcIdSettingsFor(String calcId) - { - return calcIdParams.get(calcId); - } - - public void setCalcIdSettingsFor(String calcId, AutoCalcSetting settings, - boolean needsUpdate) - { - calcIdParams.put(calcId, settings); - // TODO: create a restart list to trigger any calculations that need to be - // restarted after load - // calculator.getRegisteredWorkersOfClass(settings.getWorkerClass()) - if (needsUpdate) - { - Cache.log.debug("trigger update for " + calcId); - } - } }