X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=0dcd5435597d10490726874fdff848d8710912b8;hb=567c2595554096f10feab130153f97286f3f7d80;hp=7cf7be05fddf93fa6070f30e7d96362b10fcd248;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java index 7cf7be0..0dcd543 100644 --- a/src/jalview/appletgui/AlignViewport.java +++ b/src/jalview/appletgui/AlignViewport.java @@ -20,86 +20,47 @@ */ package jalview.appletgui; -import jalview.analysis.NJTree; +import jalview.analysis.TreeModel; import jalview.api.AlignViewportI; +import jalview.api.FeatureSettingsModelI; import jalview.bin.JalviewLite; +import jalview.commands.CommandI; import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; +import jalview.datamodel.SearchResults; +import jalview.datamodel.SearchResultsI; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; +import jalview.renderer.ResidueShader; import jalview.schemes.ColourSchemeProperty; import jalview.schemes.UserColourScheme; import jalview.structure.SelectionSource; +import jalview.structure.StructureSelectionManager; import jalview.structure.VamsasSource; import jalview.viewmodel.AlignmentViewport; +import jalview.viewmodel.ViewportRanges; import java.awt.Font; -import java.util.Stack; public class AlignViewport extends AlignmentViewport implements - AlignViewportI, SelectionSource, VamsasSource + SelectionSource { - int startRes; - - int endRes; - - int startSeq; - - int endSeq; - boolean cursorMode = false; - boolean showJVSuffix = true; - - boolean showText = true; - - boolean showColourText = false; - - boolean showBoxes = true; - - boolean wrapAlignment = false; - - boolean renderGaps = true; - - boolean showAnnotation = true; - - boolean upperCasebold = false; - - int charHeight; - - int charWidth; - - int wrappedWidth; - Font font = new Font("SansSerif", Font.PLAIN, 10); boolean validCharWidth = true; - int threshold; - - int increment; - - NJTree currentTree = null; - - boolean scaleAboveWrapped = true; - - boolean scaleLeftWrapped = true; - - boolean scaleRightWrapped = true; - - boolean showHiddenMarkers = true; + TreeModel currentTree = null; public jalview.bin.JalviewLite applet; boolean MAC = false; - Stack historyList = new Stack(); - - Stack redoList = new Stack(); - private AnnotationColumnChooser annotationColumnSelectionState; + @Override public void finalize() { applet = null; @@ -110,15 +71,14 @@ public class AlignViewport extends AlignmentViewport implements public AlignViewport(AlignmentI al, JalviewLite applet) { + super(); calculator = new jalview.workers.AlignCalcManager(); this.applet = applet; - setAlignment(al); + alignment = al; + ranges = new ViewportRanges(this.alignment); // we always pad gaps this.setPadGaps(true); - this.startRes = 0; - this.endRes = al.getWidth() - 1; - this.startSeq = 0; - this.endSeq = al.getHeight() - 1; + if (applet != null) { // get the width and height scaling factors if they were specified @@ -138,7 +98,7 @@ public class AlignViewport extends AlignmentViewport implements + widthScale + "). Ignoring."); widthScale = 1; } - if (applet.debug) + if (JalviewLite.debug) { System.err .println("Alignment character width scaling factor is now " @@ -161,7 +121,7 @@ public class AlignViewport extends AlignmentViewport implements + heightScale + "). Ignoring."); heightScale = 1; } - if (applet.debug) + if (JalviewLite.debug) { System.err .println("Alignment character height scaling factor is now " @@ -175,10 +135,11 @@ public class AlignViewport extends AlignmentViewport implements if (applet != null) { - showJVSuffix = applet.getDefaultParameter("showFullId", showJVSuffix); + setShowJVSuffix(applet.getDefaultParameter("showFullId", + getShowJVSuffix())); - showAnnotation = applet.getDefaultParameter("showAnnotation", - showAnnotation); + setShowAnnotation(applet.getDefaultParameter("showAnnotation", + isShowAnnotation())); showConservation = applet.getDefaultParameter("showConservation", showConservation); @@ -188,22 +149,25 @@ public class AlignViewport extends AlignmentViewport implements showConsensus = applet.getDefaultParameter("showConsensus", showConsensus); - showUnconserved = applet.getDefaultParameter("showUnconserved", - showUnconserved); + setShowUnconserved(applet.getDefaultParameter("showUnconserved", + getShowUnconserved())); + + setScaleProteinAsCdna(applet.getDefaultParameter( + "scaleProteinAsCdna", isScaleProteinAsCdna())); String param = applet.getParameter("upperCase"); if (param != null) { if (param.equalsIgnoreCase("bold")) { - upperCasebold = true; + setUpperCasebold(true); } } sortByTree = applet.getDefaultParameter("sortByTree", sortByTree); - followHighlight = applet.getDefaultParameter("automaticScrolling", - followHighlight); - followSelection = followHighlight; + setFollowHighlight(applet.getDefaultParameter("automaticScrolling", + isFollowHighlight())); + followSelection = isFollowHighlight(); showSequenceLogo = applet.getDefaultParameter("showSequenceLogo", showSequenceLogo); @@ -225,8 +189,13 @@ public class AlignViewport extends AlignmentViewport implements if (applet != null) { - String colour = applet.getParameter("defaultColour"); - + String colour = al.isNucleotide() ? applet + .getParameter("defaultColourNuc") : applet + .getParameter("defaultColourProt"); + if (colour == null) + { + colour = applet.getParameter("defaultColour"); + } if (colour == null) { colour = applet.getParameter("userDefinedColour"); @@ -238,18 +207,19 @@ public class AlignViewport extends AlignmentViewport implements if (colour != null) { - globalColourScheme = ColourSchemeProperty.getColour(alignment, - colour); - if (globalColourScheme != null) + residueShading = new ResidueShader( + ColourSchemeProperty.getColourScheme(alignment, colour)); + if (residueShading != null) { - globalColourScheme.setConsensus(hconsensus); + residueShading.setConsensus(hconsensus); } } if (applet.getParameter("userDefinedColour") != null) { - ((UserColourScheme) globalColourScheme).parseAppletParameter(applet - .getParameter("userDefinedColour")); + residueShading = new ResidueShader( + new UserColourScheme( + applet.getParameter("userDefinedColour"))); } } initAutoAnnotation(); @@ -272,7 +242,7 @@ public class AlignViewport extends AlignmentViewport implements { return null; } - StringBuffer seqs = new StringBuffer(); + StringBuilder seqs = new StringBuilder(consensus.annotations.length); for (int i = 0; i < consensus.annotations.length; i++) { if (consensus.annotations[i] != null) @@ -293,64 +263,6 @@ public class AlignViewport extends AlignmentViewport implements return sq; } - public int getStartRes() - { - return startRes; - } - - public int getEndRes() - { - return endRes; - } - - public int getStartSeq() - { - return startSeq; - } - - public void setStartRes(int res) - { - this.startRes = res; - } - - public void setStartSeq(int seq) - { - this.startSeq = seq; - } - - public void setEndRes(int res) - { - if (res > alignment.getWidth() - 1) - { - // log.System.out.println(" Corrected res from " + res + " to maximum " + - // (alignment.getWidth()-1)); - res = alignment.getWidth() - 1; - } - if (res < 0) - { - res = 0; - } - this.endRes = res; - } - - public void setEndSeq(int seq) - { - if (seq > alignment.getHeight()) - { - seq = alignment.getHeight(); - } - if (seq < 0) - { - seq = 0; - } - this.endSeq = seq; - } - - public int getEndSeq() - { - return endSeq; - } - java.awt.Frame nullFrame; protected FeatureSettings featureSettings = null; @@ -368,13 +280,13 @@ public class AlignViewport extends AlignmentViewport implements java.awt.FontMetrics fm = nullFrame.getGraphics().getFontMetrics(font); setCharHeight((int) (heightScale * fm.getHeight())); - charWidth = (int) (widthScale * fm.charWidth('M')); + setCharWidth((int) (widthScale * fm.charWidth('M'))); - if (upperCasebold) + if (isUpperCasebold()) { Font f2 = new Font(f.getName(), Font.BOLD, f.getSize()); fm = nullFrame.getGraphics().getFontMetrics(f2); - charWidth = (int) (widthScale * (fm.stringWidth("MMMMMMMMMMM") / 10)); + setCharWidth((int) (widthScale * (fm.stringWidth("MMMMMMMMMMM") / 10))); } } @@ -383,186 +295,21 @@ public class AlignViewport extends AlignmentViewport implements return font; } - public int getCharWidth() - { - return charWidth; - } - - public void setCharHeight(int h) - { - this.charHeight = h; - } - - public int getCharHeight() - { - return charHeight; - } - - public void setWrappedWidth(int w) - { - this.wrappedWidth = w; - } - - public int getwrappedWidth() - { - return wrappedWidth; - } - - public AlignmentI getAlignment() - { - return alignment; - } - - public void setAlignment(AlignmentI align) - { - this.alignment = align; - } - - public void setWrapAlignment(boolean state) - { - wrapAlignment = state; - } - - public void setShowText(boolean state) - { - showText = state; - } - - public void setRenderGaps(boolean state) - { - renderGaps = state; - } - - public boolean getColourText() - { - return showColourText; - } - - public void setColourText(boolean state) - { - showColourText = state; - } - - public void setShowBoxes(boolean state) - { - showBoxes = state; - } - - public boolean getWrapAlignment() - { - return wrapAlignment; - } - - public boolean getShowText() - { - return showText; - } - - public boolean getShowBoxes() - { - return showBoxes; - } - - public char getGapCharacter() - { - return getAlignment().getGapCharacter(); - } - - public void setGapCharacter(char gap) - { - if (getAlignment() != null) - { - getAlignment().setGapCharacter(gap); - } - } - public void resetSeqLimits(int height) { - setEndSeq(height / getCharHeight()); + ranges.setEndSeq(height / getCharHeight()); } - public void setCurrentTree(NJTree tree) + public void setCurrentTree(TreeModel tree) { currentTree = tree; } - public NJTree getCurrentTree() + public TreeModel getCurrentTree() { return currentTree; } - public boolean getShowJVSuffix() - { - return showJVSuffix; - } - - public void setShowJVSuffix(boolean b) - { - showJVSuffix = b; - } - - public boolean getShowAnnotation() - { - return showAnnotation; - } - - public void setShowAnnotation(boolean b) - { - showAnnotation = b; - } - - public boolean getScaleAboveWrapped() - { - return scaleAboveWrapped; - } - - public boolean getScaleLeftWrapped() - { - return scaleLeftWrapped; - } - - public boolean getScaleRightWrapped() - { - return scaleRightWrapped; - } - - public void setScaleAboveWrapped(boolean b) - { - scaleAboveWrapped = b; - } - - public void setScaleLeftWrapped(boolean b) - { - scaleLeftWrapped = b; - } - - public void setScaleRightWrapped(boolean b) - { - scaleRightWrapped = b; - } - - public void setIgnoreGapsConsensus(boolean b) - { - ignoreGapsInConsensusCalculation = b; - updateConsensus(null); - if (globalColourScheme != null) - { - globalColourScheme.setThreshold(globalColourScheme.getThreshold(), - ignoreGapsInConsensusCalculation); - - } - } - - public boolean getShowHiddenMarkers() - { - return showHiddenMarkers; - } - - public void setShowHiddenMarkers(boolean show) - { - showHiddenMarkers = show; - } - boolean centreColumnLabels; public boolean getCentreColumnLabels() @@ -570,13 +317,6 @@ public class AlignViewport extends AlignmentViewport implements return centreColumnLabels; } - public boolean followHighlight = true; - - public boolean getFollowHighlight() - { - return followHighlight; - } - public boolean followSelection = true; /** @@ -588,47 +328,28 @@ public class AlignViewport extends AlignmentViewport implements return followSelection; } + @Override public void sendSelection() { - jalview.structure.StructureSelectionManager - .getStructureSelectionManager(applet).sendSelection( - new SequenceGroup(getSelectionGroup()), - new ColumnSelection(getColumnSelection()), this); + getStructureSelectionManager().sendSelection( + new SequenceGroup(getSelectionGroup()), + new ColumnSelection(getColumnSelection()), this); } /** - * 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. + * Returns an instance of the StructureSelectionManager scoped to this applet + * instance. * - * @param sg - * @param wholewidth + * @return */ - public void expandColSelection(SequenceGroup sg, boolean wholewidth) + @Override + public StructureSelectionManager getStructureSelectionManager() { - int sgs, sge; - if (sg != null - && (sgs = sg.getStartRes()) >= 0 - && sg.getStartRes() <= (sge = sg.getEndRes()) - && (colSel == null || colSel.getSelected() == null || colSel - .getSelected().size() == 0)) - { - 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 jalview.structure.StructureSelectionManager + .getStructureSelectionManager(applet); } + @Override public boolean isNormaliseSequenceLogo() { return normaliseSequenceLogo; @@ -643,6 +364,7 @@ public class AlignViewport extends AlignmentViewport implements * * @return true if alignment characters should be displayed */ + @Override public boolean isValidCharWidth() { return validCharWidth; @@ -659,4 +381,80 @@ public class AlignViewport extends AlignmentViewport implements this.annotationColumnSelectionState = annotationColumnSelectionState; } + @Override + public void mirrorCommand(CommandI command, boolean undo, + StructureSelectionManager ssm, VamsasSource source) + { + // TODO refactor so this can be pulled up to superclass or controller + /* + * 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) + { + mappedCommand.doCommand(null); + firePropertyChange("alignment", null, getAlignment().getSequences()); + + // ap.scalePanelHolder.repaint(); + // ap.repaint(); + } + } + + @Override + public VamsasSource getVamsasSource() + { + return this; + } + + /** + * If this viewport has a (Protein/cDNA) complement, then scroll the + * complementary alignment to match this one. + */ + public void scrollComplementaryAlignment(AlignmentPanel complementPanel) + { + if (complementPanel == null) + { + return; + } + + /* + * 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. + */ + SearchResultsI sr = new SearchResults(); + int seqOffset = findComplementScrollTarget(sr); + if (!sr.isEmpty()) + { + complementPanel.setFollowingComplementScroll(true); + complementPanel.scrollToCentre(sr, seqOffset); + } + } + + /** + * Applies the supplied feature settings descriptor to currently known + * features. This supports an 'initial configuration' of feature colouring + * based on a preset or user favourite. This may then be modified in the usual + * way using the Feature Settings dialogue. + * + * @param featureSettings + */ + @Override + public void applyFeaturesStyle(FeatureSettingsModelI featureSettings) + { + // TODO implement for applet + } + }