X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=6c7b39af344743c7b907d19ed74a6bb63295584a;hb=refs%2Fheads%2Ffeatures%2Fhmmer_statistics;hp=e4e3e1777a886f3ec492a021878d43b9c6a184fc;hpb=ca431c5b3c0febeecdf541537070d5141d3b531a;p=jalview.git diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java index e4e3e17..6c7b39a 100644 --- a/src/jalview/appletgui/AlignViewport.java +++ b/src/jalview/appletgui/AlignViewport.java @@ -20,28 +20,32 @@ */ 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.HiddenColumns; 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.CommandListener; import jalview.structure.SelectionSource; import jalview.structure.StructureSelectionManager; import jalview.structure.VamsasSource; import jalview.viewmodel.AlignmentViewport; import java.awt.Font; +import java.awt.FontMetrics; public class AlignViewport extends AlignmentViewport implements - SelectionSource, VamsasSource, CommandListener + SelectionSource { boolean cursorMode = false; @@ -49,7 +53,7 @@ public class AlignViewport extends AlignmentViewport implements boolean validCharWidth = true; - NJTree currentTree = null; + TreeModel currentTree = null; public jalview.bin.JalviewLite applet; @@ -57,6 +61,7 @@ public class AlignViewport extends AlignmentViewport implements private AnnotationColumnChooser annotationColumnSelectionState; + @Override public void finalize() { applet = null; @@ -67,16 +72,13 @@ public class AlignViewport extends AlignmentViewport implements public AlignViewport(AlignmentI al, JalviewLite applet) { - super(); + super(al); calculator = new jalview.workers.AlignCalcManager(); this.applet = applet; - alignment = al; + // 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 @@ -127,7 +129,7 @@ public class AlignViewport extends AlignmentViewport implements } } } - setFont(font); + setFont(font, true); MAC = new jalview.util.Platform().isAMac(); @@ -147,6 +149,9 @@ public class AlignViewport extends AlignmentViewport implements showConsensus = applet.getDefaultParameter("showConsensus", showConsensus); + showOccupancy = applet.getDefaultParameter("showOccupancy", + showOccupancy); + setShowUnconserved(applet.getDefaultParameter("showUnconserved", getShowUnconserved())); @@ -187,8 +192,13 @@ 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"); @@ -200,18 +210,19 @@ 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(); @@ -261,7 +272,11 @@ public class AlignViewport extends AlignmentViewport implements private float heightScale = 1, widthScale = 1; - public void setFont(Font f) + /** + * {@inheritDoc} + */ + @Override + public void setFont(Font f, boolean setGrid) { font = f; if (nullFrame == null) @@ -270,14 +285,17 @@ public class AlignViewport extends AlignmentViewport implements nullFrame.addNotify(); } - java.awt.FontMetrics fm = nullFrame.getGraphics().getFontMetrics(font); - setCharHeight((int) (heightScale * fm.getHeight())); - setCharWidth((int) (widthScale * fm.charWidth('M'))); + if (setGrid) + { + FontMetrics fm = nullFrame.getGraphics().getFontMetrics(font); + setCharHeight((int) (heightScale * fm.getHeight())); + setCharWidth((int) (widthScale * fm.charWidth('M'))); + } if (isUpperCasebold()) { Font f2 = new Font(f.getName(), Font.BOLD, f.getSize()); - fm = nullFrame.getGraphics().getFontMetrics(f2); + FontMetrics fm = nullFrame.getGraphics().getFontMetrics(f2); setCharWidth((int) (widthScale * (fm.stringWidth("MMMMMMMMMMM") / 10))); } } @@ -287,23 +305,21 @@ public class AlignViewport extends AlignmentViewport implements return font; } - 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; } - boolean centreColumnLabels; public boolean getCentreColumnLabels() @@ -322,11 +338,13 @@ public class AlignViewport extends AlignmentViewport implements return followSelection; } + @Override public void sendSelection() { getStructureSelectionManager().sendSelection( - new SequenceGroup(getSelectionGroup()), - new ColumnSelection(getColumnSelection()), this); + new SequenceGroup(getSelectionGroup()), + new ColumnSelection(getColumnSelection()), + new HiddenColumns(getAlignment().getHiddenColumns()), this); } /** @@ -342,39 +360,7 @@ public class AlignViewport extends AlignmentViewport implements .getStructureSelectionManager(applet); } - /** - * synthesize a column selection if none exists so it covers the given - * selection group. if wholewidth is false, no column selection is made if the - * selection group covers the whole alignment width. - * - * @param sg - * @param wholewidth - */ - public void expandColSelection(SequenceGroup sg, boolean wholewidth) - { - 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); - } - } - } - + @Override public boolean isNormaliseSequenceLogo() { return normaliseSequenceLogo; @@ -389,6 +375,7 @@ public class AlignViewport extends AlignmentViewport implements * * @return true if alignment characters should be displayed */ + @Override public boolean isValidCharWidth() { return validCharWidth; @@ -458,14 +445,35 @@ public class AlignViewport extends AlignmentViewport implements * there is no complement, or it is not following highlights, or no mapping * is found, the result will be empty. */ - SearchResults sr = new SearchResults(); + SearchResultsI sr = new SearchResults(); int seqOffset = findComplementScrollTarget(sr); if (!sr.isEmpty()) { - complementPanel.setFollowingComplementScroll(true); + complementPanel.setToScrollComplementPanel(false); complementPanel.scrollToCentre(sr, seqOffset); + complementPanel.setToScrollComplementPanel(true); } } + /** + * 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 + } + + @Override + public boolean isNormaliseHMMSequenceLogo() + { + // TODO Auto-generated method stub + return normaliseHMMSequenceLogo; + } }