X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=e4593a305d4c981edae71967a0a8d2cf25ea1326;hb=f18077aa57dea5481ae537162871045f8557e2f0;hp=705f53aff8bf4744c2c880197ea5c64cc188566a;hpb=61f1a8b75ea5ce352d6214c34fbdcd58bafbbb73;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index 705f53a..e4593a3 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 ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -38,14 +38,27 @@ */ 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.Set; +import java.util.Vector; + +import javax.swing.JInternalFrame; +import javax.swing.JOptionPane; + import jalview.analysis.AlignmentUtils; -import jalview.analysis.AlignmentUtils.MappingResult; import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; import jalview.analysis.NJTree; import jalview.api.AlignViewportI; +import jalview.api.ViewStyleI; import jalview.bin.Cache; import jalview.commands.CommandI; -import jalview.commands.EditCommand; +import jalview.datamodel.AlignedCodonFrame; +import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; import jalview.datamodel.PDBEntry; @@ -62,22 +75,6 @@ import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; import jalview.ws.params.AutoCalcSetting; -import java.awt.Color; -import java.awt.Container; -import java.awt.Font; -import java.awt.Rectangle; -import java.util.ArrayDeque; -import java.util.ArrayList; -import java.util.Deque; -import java.util.Hashtable; -import java.util.List; -import java.util.Set; -import java.util.Vector; - -import javax.swing.JInternalFrame; -import javax.swing.JOptionPane; -import javax.swing.JSplitPane; - /** * DOCUMENT ME! * @@ -85,7 +82,7 @@ import javax.swing.JSplitPane; * @version $Revision: 1.141 $ */ public class AlignViewport extends AlignmentViewport implements - SelectionSource, VamsasSource, AlignViewportI, CommandListener + SelectionSource, AlignViewportI, CommandListener { int startRes; @@ -95,74 +92,28 @@ 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; - - SequenceAnnotationOrder sortAnnotationsBy = null; - - 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; - - private Deque historyList = new ArrayDeque(); - - private Deque redoList = new ArrayDeque(); - - 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. * @@ -218,16 +169,7 @@ 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(); } @@ -274,46 +216,51 @@ 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() + 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); + + } + + 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")) @@ -325,7 +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)); @@ -350,16 +297,24 @@ public class AlignViewport extends AlignmentViewport implements showConsensus = Cache.getDefault("SHOW_IDENTITY", 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) @@ -367,47 +322,9 @@ public class AlignViewport extends AlignmentViewport implements globalColourScheme.setConsensus(hconsensus); } } - - wrapAlignment = Cache.getDefault("WRAP_ALIGNMENT", false); - showUnconserved = Cache.getDefault("SHOW_UNCONSERVED", false); - sortByTree = Cache.getDefault("SORT_BY_TREE", false); - followSelection = Cache.getDefault("FOLLOW_SELECTIONS", true); - sortAnnotationsBy = SequenceAnnotationOrder.valueOf(Cache.getDefault( - Preferences.SORT_ANNOTATIONS, - SequenceAnnotationOrder.NONE.name())); - showAutocalculatedAbove = Cache.getDefault( - Preferences.SHOW_AUTOCALC_ABOVE, false); } /** - * 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. * @@ -551,105 +468,52 @@ 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; } /** @@ -676,101 +540,6 @@ 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() @@ -824,131 +593,6 @@ 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 @@ -1021,72 +665,6 @@ 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 */ @@ -1113,8 +691,9 @@ 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 @@ -1123,16 +702,6 @@ 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. @@ -1145,7 +714,6 @@ 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) @@ -1199,6 +767,10 @@ public class AlignViewport extends AlignmentViewport implements } } + /** + * Returns the (Desktop) instance of the StructureSelectionManager + */ + @Override public StructureSelectionManager getStructureSelectionManager() { return StructureSelectionManager @@ -1266,8 +838,6 @@ public class AlignViewport extends AlignmentViewport implements private Hashtable calcIdParams = new Hashtable(); - private boolean showAutocalculatedAbove; - public AutoCalcSetting getCalcIdSettingsFor(String calcId) { return calcIdParams.get(calcId); @@ -1286,26 +856,6 @@ public class AlignViewport extends AlignmentViewport implements } } - protected SequenceAnnotationOrder getSortAnnotationsBy() - { - return sortAnnotationsBy; - } - - protected void setSortAnnotationsBy(SequenceAnnotationOrder sortAnnotationsBy) - { - this.sortAnnotationsBy = sortAnnotationsBy; - } - - protected boolean isShowAutocalculatedAbove() - { - return showAutocalculatedAbove; - } - - protected void setShowAutocalculatedAbove(boolean showAutocalculatedAbove) - { - this.showAutocalculatedAbove = showAutocalculatedAbove; - } - /** * Method called when another alignment's edit (or possibly other) command is * broadcast to here. @@ -1325,99 +875,36 @@ public class AlignViewport extends AlignmentViewport implements */ @Override public void mirrorCommand(CommandI command, boolean undo, - StructureSelectionManager ssm) + StructureSelectionManager ssm, VamsasSource source) { /* - * Only EditCommand is currently handled by listeners. + * Do nothing unless we are a 'complement' of the source. May replace this + * with direct calls not via SSM. */ - if (!(command instanceof EditCommand)) + if (source instanceof AlignViewportI + && ((AlignViewportI) source).getCodingComplement() == this) { - return; + // ok to continue; } - EditCommand edit = (EditCommand) command; - - List seqs = getAlignment().getSequences(); - EditCommand mappedCommand = ssm.mapEditCommand(edit, undo, seqs, - getGapCharacter()); - AlignmentI[] views = getAlignPanel().alignFrame.getViewAlignments(); - mappedCommand.performEdit(0, 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) + else { - this.historyList.push(command); - broadcastCommand(command, false); + return; } - } - - 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) + CommandI mappedCommand = ssm.mapCommand(command, undo, getAlignment(), + getGapCharacter()); + if (mappedCommand != null) { - this.redoList.push(command); + AlignmentI[] views = getAlignPanel().alignFrame.getViewAlignments(); + mappedCommand.doCommand(views); + getAlignPanel().alignmentChanged(); } - 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 panel linking cDNA and - * protein. + * may give the user the option to open a new frame, or split panel, with cDNA + * and protein linked. * * @param al * @param title @@ -1426,6 +913,10 @@ public class AlignViewport extends AlignmentViewport implements { // 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 @@ -1434,18 +925,15 @@ public class AlignViewport extends AlignmentViewport implements * 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()) + if (AlignmentUtils.isMappable(al, getAlignment())) { - final Set sequenceNames = getAlignment().getSequenceNames(); - sequenceNames.retainAll(al.getSequenceNames()); - if (!sequenceNames.isEmpty()) // at least one sequence name in both + if (openLinkedAlignment(al, title)) { - if (openLinkedAlignment(al, title)) - { - return; - } + 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++) { @@ -1453,15 +941,16 @@ public class AlignViewport extends AlignmentViewport implements } // 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 - - * either because the user declined the offer, or because no mapping could be - * made. + * alignment. Returns true if the new alignment was opened, false if not, + * because the user declined the offer. * * @param title */ @@ -1472,16 +961,11 @@ public class AlignViewport extends AlignmentViewport implements MessageManager.getString("label.split_window"), MessageManager.getString("label.new_window"), }; final String question = JvSwingUtils.wrapTooltip(true, - MessageManager.getString("label.open_linked_alignment?")); + MessageManager.getString("label.open_split_window?")); int response = JOptionPane.showOptionDialog(Desktop.desktop, question, - MessageManager.getString("label.open_linked_alignment"), + MessageManager.getString("label.open_split_window"), JOptionPane.DEFAULT_OPTION, JOptionPane.PLAIN_MESSAGE, null, options, options[0]); - // int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop, - // question, - // MessageManager.getString("label.open_linked_alignment"), - // JOptionPane.YES_NO_OPTION, - // JOptionPane.QUESTION_MESSAGE); if (response != 1 && response != 2) { @@ -1494,13 +978,20 @@ public class AlignViewport extends AlignmentViewport implements * Create the AlignFrame first (which creates the new alignment's datasets), * before attempting sequence mapping. */ - AlignFrame alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH, + AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); + newAlignFrame.setTitle(title); - final AlignmentI protein = al.isNucleotide() ? getAlignment() : al; - final AlignmentI cdna = al.isNucleotide() ? al : getAlignment(); + /* + * 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; - alignFrame.statusBar.setText(MessageManager.formatMessage( + newAlignFrame.statusBar.setText(MessageManager.formatMessage( "label.successfully_loaded_file", new Object[] { title })); @@ -1510,52 +1001,25 @@ public class AlignViewport extends AlignmentViewport implements // { // alignFrame.setFileName(file, format); // } + if (openInNewWindow) { - /* - * open in new window - */ - Desktop.addInternalFrame(alignFrame, title, AlignFrame.DEFAULT_WIDTH, + Desktop.addInternalFrame(newAlignFrame, title, + AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); } /* - * Try to find mappings for at least one sequence. + * 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. */ - MappingResult mapped = AlignmentUtils.mapProteinToCdna(protein, cdna); - if (mapped == MappingResult.Mapped) - { - - /* - * 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()); - - /* - * Set the cDNA to listen for edits on the protein. - */ - ssm.addCommandListener(al.isNucleotide() ? alignFrame.getViewport() - : this); - } - 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); - } + AlignmentUtils.mapProteinToCdna(protein, cdna); try { - alignFrame.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", + newAlignFrame.setMaximum(jalview.bin.Cache.getDefault( + "SHOW_FULLSCREEN", false)); } catch (java.beans.PropertyVetoException ex) { @@ -1563,25 +1027,103 @@ public class AlignViewport extends AlignmentViewport implements if (openSplitPane) { - /* - * Open in split pane. Original sequence above, new one below. - */ - JInternalFrame splitFrame = new JInternalFrame(); - splitFrame.setSize(AlignFrame.DEFAULT_WIDTH, - AlignFrame.DEFAULT_HEIGHT); - // TODO not quite right to 'move' AlignPanel from 'this' to the split - // pane - // TODO probably want linked editing set up here - JSplitPane splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT, - getAlignPanel(), alignFrame.alignPanel); - splitPane.setDividerLocation(0.5d); - splitFrame.setSize(AlignFrame.DEFAULT_WIDTH, - AlignFrame.DEFAULT_HEIGHT); - splitFrame.add(splitPane); - Desktop.addInternalFrame(splitFrame, title, AlignFrame.DEFAULT_WIDTH, - AlignFrame.DEFAULT_HEIGHT); + 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; + } }