X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=d84d3a38cb457a876edf3afef8ed1b77fd307b92;hb=9612728299dc4c2242a6a968875a194624983920;hp=e9829bb7d31ce7d454483915e0fd43cad1f5d7a4;hpb=2f4f1d8fb6878271b64f327bc58c895f458137af;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index e9829bb..d84d3a3 100644 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -1,19 +1,21 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) - * 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. * * 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. + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . * The Jalview Authors are detailed in the 'AUTHORS' file. */ /* @@ -36,34 +38,48 @@ */ package jalview.gui; +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.List; +import java.util.Set; +import java.util.Vector; + +import javax.swing.JInternalFrame; +import javax.swing.JOptionPane; + +import jalview.analysis.AlignmentUtils; +import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; import jalview.analysis.NJTree; import jalview.api.AlignViewportI; +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.HiddenSequences; 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.Comparison; +import jalview.util.MappingUtils; +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.ArrayList; -import java.util.Hashtable; -import java.util.Stack; -import java.util.Vector; - /** * DOCUMENT ME! * @@ -71,7 +87,7 @@ import java.util.Vector; * @version $Revision: 1.141 $ */ public class AlignViewport extends AlignmentViewport implements - SelectionSource, VamsasSource, AlignViewportI + SelectionSource, AlignViewportI, CommandListener { int startRes; @@ -81,72 +97,28 @@ public class AlignViewport extends AlignmentViewport implements 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; - /** - * Keys are the feature types which are currently visible. Note: Values are - * not used! - */ - Hashtable featuresDisplayed = null; - 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; - - boolean rightAlignIds = false; + /* + * 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; + private AnnotationColumnChooser annotationColumnSelectionState; /** * Creates a new AlignViewport object. * @@ -202,16 +174,7 @@ 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(); } @@ -258,46 +221,55 @@ 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, false)); + } + + 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")) @@ -309,7 +281,7 @@ 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)); @@ -332,22 +304,26 @@ 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) @@ -355,44 +331,9 @@ 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. * @@ -536,105 +477,52 @@ public class AlignViewport extends AlignmentViewport implements return endSeq; } + boolean validCharWidth; + /** - * DOCUMENT ME! + * update view settings with the given font. You may need to call + * alignPanel.fontChanged to update the layout geometry * - * @param f - * DOCUMENT ME! + * @param setGrid + * when true, charWidth/height is set according to font mentrics */ - public void setFont(Font f) + public void setFont(Font f, boolean setGrid) { font = f; Container c = new Container(); java.awt.FontMetrics fm = c.getFontMetrics(font); - setCharHeight(fm.getHeight()); - setCharWidth(fm.charWidth('M')); - validCharWidth = true; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public Font getFont() - { - return font; - } - - /** - * DOCUMENT ME! - * - * @param w - * DOCUMENT ME! - */ - public void setCharWidth(int w) - { - this.charWidth = w; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getCharWidth() - { - return charWidth; - } - - /** - * DOCUMENT ME! - * - * @param h - * DOCUMENT ME! - */ - public void setCharHeight(int h) - { - this.charHeight = h; - } + 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()); - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getCharHeight() - { - return charHeight; + validCharWidth = true; } - /** - * DOCUMENT ME! - * - * @param w - * DOCUMENT ME! - */ - public void setWrappedWidth(int w) + @Override + public void setViewStyle(ViewStyleI settingsForView) { - this.wrappedWidth = w; - } + super.setViewStyle(settingsForView); + setFont(new Font(viewStyle.getFontName(), viewStyle.getFontStyle(), + viewStyle.getFontSize()), false); - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getWrappedWidth() - { - return wrappedWidth; } - /** * DOCUMENT ME! * * @return DOCUMENT ME! */ - public AlignmentI getAlignment() + public Font getFont() { - return alignment; + return font; } /** @@ -661,101 +549,6 @@ public class AlignViewport extends AlignmentViewport implements /** * DOCUMENT ME! * - * @param state - * DOCUMENT ME! - */ - public void setWrapAlignment(boolean state) - { - wrapAlignment = state; - } - - /** - * DOCUMENT ME! - * - * @param state - * DOCUMENT ME! - */ - public void setShowText(boolean state) - { - showText = state; - } - - /** - * 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() @@ -809,131 +602,6 @@ public class AlignViewport extends AlignmentViewport implements } /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getShowJVSuffix() - { - return showJVSuffix; - } - - /** - * DOCUMENT ME! - * - * @param b - * DOCUMENT ME! - */ - public void setShowJVSuffix(boolean b) - { - showJVSuffix = b; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getShowAnnotation() - { - return showAnnotation; - } - - /** - * DOCUMENT ME! - * - * @param b - * DOCUMENT ME! - */ - public void setShowAnnotation(boolean b) - { - showAnnotation = b; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getScaleAboveWrapped() - { - return scaleAboveWrapped; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getScaleLeftWrapped() - { - return scaleLeftWrapped; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getScaleRightWrapped() - { - return scaleRightWrapped; - } - - /** - * DOCUMENT ME! - * - * @param b - * DOCUMENT ME! - */ - public void setScaleAboveWrapped(boolean b) - { - scaleAboveWrapped = b; - } - - /** - * DOCUMENT ME! - * - * @param b - * DOCUMENT ME! - */ - public void setScaleLeftWrapped(boolean b) - { - scaleLeftWrapped = b; - } - - /** - * DOCUMENT ME! - * - * @param b - * DOCUMENT ME! - */ - public void setScaleRightWrapped(boolean b) - { - scaleRightWrapped = b; - } - - public void setDataset(boolean b) - { - isDataset = b; - } - - public boolean isDataset() - { - return isDataset; - } - - public boolean getShowHiddenMarkers() - { - return showHiddenMarkers; - } - - public void setShowHiddenMarkers(boolean show) - { - showHiddenMarkers = show; - } - - /** * returns the visible column regions of the alignment * * @param selectedRegionOnly @@ -967,8 +635,10 @@ public class AlignViewport extends AlignmentViewport implements { // TODO: JAL-1126 if (historyList == null || redoList == null) + { return new long[] { -1, -1 }; + } return new long[] { historyList.hashCode(), this.redoList.hashCode() }; } @@ -1004,73 +674,6 @@ public class AlignViewport extends AlignmentViewport implements 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 if Database References are to be displayed on tooltips. - */ - public boolean isShowDbRefs() - { - return showdbrefs; - } - - /** - * - * @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 - */ - public void setShowNpFeats(boolean show) - { - shownpfeats = show; - } - - /** - * - * @return true if view has hidden rows - */ - public boolean hasHiddenRows() - { - return hasHiddenRows; - } - - /** - * - * @return true if view has hidden columns - */ - public boolean hasHiddenColumns() - { - return hasHiddenColumns; - } - /** * when set, view will scroll to show the highlighted position */ @@ -1097,8 +700,9 @@ public class AlignViewport extends AlignmentViewport implements return followSelection; } - boolean showSeqFeaturesHeight; - + /** + * Send the current selection to be broadcast to any selection listeners. + */ public void sendSelection() { jalview.structure.StructureSelectionManager @@ -1107,16 +711,6 @@ public class AlignViewport extends AlignmentViewport implements new ColumnSelection(getColumnSelection()), this); } - public void setShowSequenceFeaturesHeight(boolean selected) - { - showSeqFeaturesHeight = selected; - } - - public boolean getShowSequenceFeaturesHeight() - { - return showSeqFeaturesHeight; - } - /** * return the alignPanel containing the given viewport. Use this to get the * components currently handling the given viewport. @@ -1129,7 +723,6 @@ public class AlignViewport extends AlignmentViewport implements { AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(this .getSequenceSetId()); - AlignmentPanel ap = null; for (int p = 0; aps != null && p < aps.length; p++) { if (aps[p].av == this) @@ -1183,6 +776,10 @@ public class AlignViewport extends AlignmentViewport implements } } + /** + * Returns the (Desktop) instance of the StructureSelectionManager + */ + @Override public StructureSelectionManager getStructureSelectionManager() { return StructureSelectionManager @@ -1206,7 +803,9 @@ public class AlignViewport extends AlignmentViewport implements Vector pdbs = alignment.getSequenceAt(i).getDatasetSequence() .getPDBId(); if (pdbs == null) + { continue; + } SequenceI sq; for (int p = 0; p < pdbs.size(); p++) { @@ -1214,7 +813,9 @@ public class AlignViewport extends AlignmentViewport implements if (p1.getId().equals(pdb.getId())) { if (!seqs.contains(sq = alignment.getSequenceAt(i))) + { seqs.add(sq); + } continue; } @@ -1263,4 +864,345 @@ public class AlignViewport extends AlignmentViewport implements Cache.log.debug("trigger update for " + calcId); } } + + /** + * 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: + * + * + * @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; + } + + CommandI mappedCommand = ssm.mapCommand(command, undo, getAlignment(), + getGapCharacter()); + if (mappedCommand != null) + { + AlignmentI[] views = getAlignPanel().alignFrame.getViewAlignments(); + mappedCommand.doCommand(views); + getAlignPanel().alignmentChanged(); + } + } + + /** + * 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 + + // 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 + + // 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 (AlignmentUtils.isMappable(al, getAlignment())) + { + if (openLinkedAlignment(al, title)) + { + return; + } + } + // TODO: JAL-407 regardless of above - identical sequences (based on ID and + // provenance) should share the same dataset sequence + + 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? + // JBPComment: this repositions the view to show the new sequences + // JBPComment: so it is needed for UX + 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_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) + { + 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); + newAlignFrame.setTitle(title); + + /* + * 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; + + 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); + } + + /* + * 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. + */ + AlignmentUtils.mapProteinToCdna(protein, cdna); + + try + { + newAlignFrame.setMaximum(jalview.bin.Cache.getDefault( + "SHOW_FULLSCREEN", + false)); + } catch (java.beans.PropertyVetoException ex) + { + } + + if (openSplitPane) + { + protein = openSplitFrame(newAlignFrame, thisAlignment, + protein.getCodonFrames()); + } + + /* + * Register the mappings (held on the protein alignment) with the + * StructureSelectionManager (for mouseover linking). + */ + final StructureSelectionManager ssm = StructureSelectionManager + .getStructureSelectionManager(Desktop.instance); + ssm.addMappings(protein.getCodonFrames()); + + return true; + } + + /** + * Helper method to open a new SplitFrame holding linked dna and protein + * alignments. + * + * @param newAlignFrame + * containing a new alignment to be shown + * @param complement + * cdna/protein complement alignment to show in the other split half + * @param mappings + * @return the protein alignment in the split frame + */ + protected AlignmentI openSplitFrame(AlignFrame newAlignFrame, + AlignmentI complement, Set mappings) + { + /* + * Open in split pane. DNA sequence above, protein below. + */ + AlignFrame copyMe = new AlignFrame(complement, + AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); + copyMe.setTitle(getAlignPanel().alignFrame.getTitle()); + + AlignmentI al = newAlignFrame.viewport.getAlignment(); + final AlignFrame proteinFrame = al.isNucleotide() ? copyMe + : newAlignFrame; + final AlignFrame cdnaFrame = al.isNucleotide() ? newAlignFrame + : copyMe; + AlignmentI protein = proteinFrame.viewport.getAlignment(); + protein.setCodonFrames(mappings); + + cdnaFrame.setVisible(true); + proteinFrame.setVisible(true); + String linkedTitle = MessageManager + .getString("label.linked_view_title"); + JInternalFrame splitFrame = new SplitFrame(cdnaFrame, proteinFrame); + Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1); + + return protein; + } + + public AnnotationColumnChooser getAnnotationColumnSelectionState() + { + return annotationColumnSelectionState; + } + + public void setAnnotationColumnSelectionState( + AnnotationColumnChooser currentAnnotationColumnSelectionState) + { + this.annotationColumnSelectionState = currentAnnotationColumnSelectionState; + } + + @Override + public void setIdWidth(int i) + { + 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 Rectangle getExplodedGeometry() + { + return explodedGeometry; + } + + public void setExplodedGeometry(Rectangle explodedPosition) + { + this.explodedGeometry = explodedPosition; + } + + public boolean isGatherViewsHere() + { + return gatherViewsHere; + } + + public void setGatherViewsHere(boolean gatherViewsHere) + { + this.gatherViewsHere = gatherViewsHere; + } + + /** + * If this viewport has a (Protein/cDNA) complement, then scroll the + * complementary alignment to match this one. + * + * @param horizontal + * true for horizontal scroll event, false for vertical + */ + public void scrollComplementaryAlignment(boolean horizontal) + { + /* + * If no complement, or it is not following scrolling, do nothing. + */ + // TODO pull up followHighlight to AlignmentViewport/AlignViewportI + final AlignViewport codingComplement = (AlignViewport) getCodingComplement(); + if (codingComplement == null || !codingComplement.followHighlight) + { + return; + } + boolean iAmProtein = !getAlignment().isNucleotide(); + AlignmentI proteinAlignment = iAmProtein ? getAlignment() + : codingComplement.getAlignment(); + if (proteinAlignment == null) + { + return; + } + final Set mappings = proteinAlignment + .getCodonFrames(); + + /* + * Heuristic: find the first mapped sequence (if any) with a non-gapped + * residue in the middle column of the visible region. Scroll the + * complementary alignment to line up the corresponding residue. + */ + int seqOffset = 0; + SequenceI sequence = null; + int middleColumn = getStartRes() + (getEndRes() - getStartRes()) / 2; + final HiddenSequences hiddenSequences = getAlignment() + .getHiddenSequences(); + for (int seqNo = getStartSeq(); seqNo < getEndSeq(); seqNo++, seqOffset++) + { + sequence = getAlignment().getSequenceAt(seqNo); + if (hiddenSequences != null && hiddenSequences.isHidden(sequence)) + { + continue; + } + if (Comparison.isGap(sequence.getCharAt(middleColumn))) + { + continue; + } + List seqMappings = MappingUtils + .findMappingsForSequence(sequence, mappings); + if (!seqMappings.isEmpty()) + { + break; + } + } + + if (sequence == null) + { + /* + * No ungapped mapped sequence in middle column - do nothing + */ + return; + } + SearchResults sr = MappingUtils.buildSearchResults(sequence, + sequence.findPosition(middleColumn), mappings); + codingComplement.getAlignPanel().scrollAsComplement(sr, seqOffset, + horizontal); + } }