X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=e4593a305d4c981edae71967a0a8d2cf25ea1326;hb=f18077aa57dea5481ae537162871045f8557e2f0;hp=e999f803f2578faa7104fbaebd840edf1ae21a0b;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index e999f80..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. * @@ -38,12 +38,28 @@ */ 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.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.PDBEntry; import jalview.datamodel.Sequence; @@ -51,21 +67,14 @@ 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.Font; -import java.awt.Rectangle; -import java.util.ArrayList; -import java.util.Hashtable; -import java.util.Stack; -import java.util.Vector; - /** * DOCUMENT ME! * @@ -73,7 +82,7 @@ import java.util.Vector; * @version $Revision: 1.141 $ */ public class AlignViewport extends AlignmentViewport implements - SelectionSource, VamsasSource, AlignViewportI + SelectionSource, AlignViewportI, CommandListener { int startRes; @@ -83,72 +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; - - 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. * @@ -204,16 +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(); } @@ -260,46 +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")) @@ -311,7 +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)); @@ -334,22 +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) @@ -357,44 +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. * @@ -538,105 +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; - } + 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! - * - * @param h - * DOCUMENT ME! - */ - public void setCharHeight(int h) - { - this.charHeight = h; + validCharWidth = true; } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getCharHeight() + @Override + public void setViewStyle(ViewStyleI settingsForView) { - return charHeight; - } + super.setViewStyle(settingsForView); + setFont(new Font(viewStyle.getFontName(), viewStyle.getFontStyle(), + viewStyle.getFontSize()), false); - /** - * DOCUMENT ME! - * - * @param w - * DOCUMENT ME! - */ - public void setWrappedWidth(int w) - { - this.wrappedWidth = w; } - /** * 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; } /** @@ -663,101 +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() @@ -811,131 +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 @@ -969,8 +626,10 @@ 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() }; } @@ -1006,73 +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 */ @@ -1099,8 +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 @@ -1109,16 +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. @@ -1131,7 +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) @@ -1185,6 +767,10 @@ public class AlignViewport extends AlignmentViewport implements } } + /** + * Returns the (Desktop) instance of the StructureSelectionManager + */ + @Override public StructureSelectionManager getStructureSelectionManager() { return StructureSelectionManager @@ -1208,7 +794,9 @@ 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++) { @@ -1216,7 +804,9 @@ public class AlignViewport extends AlignmentViewport implements if (p1.getId().equals(pdb.getId())) { if (!seqs.contains(sq = alignment.getSequenceAt(i))) + { seqs.add(sq); + } continue; } @@ -1265,4 +855,275 @@ 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: + *