X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=edacce80d36dab239b5f6b4c8d1c2649ed9dc07b;hb=b5667f39acdf309cd92881b73edfda591e0acaf4;hp=b025f648d0b6905051174fa506e2bf00e8ec612a;hpb=320c96aed11f5c396a9efd9ea83b0e35f05e21e4;p=jalview.git diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java index b025f64..edacce8 100644 --- a/src/jalview/appletgui/AlignViewport.java +++ b/src/jalview/appletgui/AlignViewport.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) * Copyright (C) $$Year-Rel$$ The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) * * This file is part of Jalview. * @@ -20,30 +20,29 @@ */ package jalview.appletgui; -import jalview.analysis.NJTree; 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 +public class AlignViewport extends AlignmentViewport + implements SelectionSource { boolean cursorMode = false; @@ -51,35 +50,27 @@ public class AlignViewport extends AlignmentViewport implements boolean validCharWidth = true; - NJTree currentTree = null; - public jalview.bin.JalviewLite applet; boolean MAC = false; private AnnotationColumnChooser annotationColumnSelectionState; - @Override - public void finalize() - { - applet = null; - quality = null; - alignment = null; - colSel = null; - } + java.awt.Frame nullFrame; + + protected FeatureSettings featureSettings = null; + + private float heightScale = 1, widthScale = 1; 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 @@ -88,21 +79,21 @@ public class AlignViewport extends AlignmentViewport implements { try { - widthScale = new Float(param).floatValue(); + widthScale = Float.valueOf(param).floatValue(); } catch (Exception e) { } if (widthScale <= 1.0) { - System.err - .println("Invalid alignment character width scaling factor (" + System.err.println( + "Invalid alignment character width scaling factor (" + widthScale + "). Ignoring."); widthScale = 1; } if (JalviewLite.debug) { - System.err - .println("Alignment character width scaling factor is now " + System.err.println( + "Alignment character width scaling factor is now " + widthScale); } } @@ -111,33 +102,33 @@ public class AlignViewport extends AlignmentViewport implements { try { - heightScale = new Float(param).floatValue(); + heightScale = Float.valueOf(param).floatValue(); } catch (Exception e) { } if (heightScale <= 1.0) { - System.err - .println("Invalid alignment character height scaling factor (" + System.err.println( + "Invalid alignment character height scaling factor (" + heightScale + "). Ignoring."); heightScale = 1; } if (JalviewLite.debug) { - System.err - .println("Alignment character height scaling factor is now " + System.err.println( + "Alignment character height scaling factor is now " + heightScale); } } } - setFont(font); + setFont(font, true); MAC = new jalview.util.Platform().isAMac(); if (applet != null) { - setShowJVSuffix(applet.getDefaultParameter("showFullId", - getShowJVSuffix())); + setShowJVSuffix( + applet.getDefaultParameter("showFullId", getShowJVSuffix())); setShowAnnotation(applet.getDefaultParameter("showAnnotation", isShowAnnotation())); @@ -150,11 +141,14 @@ public class AlignViewport extends AlignmentViewport implements showConsensus = applet.getDefaultParameter("showConsensus", showConsensus); + showOccupancy = applet.getDefaultParameter("showOccupancy", + showOccupancy); + setShowUnconserved(applet.getDefaultParameter("showUnconserved", getShowUnconserved())); - setScaleProteinAsCdna(applet.getDefaultParameter( - "scaleProteinAsCdna", isScaleProteinAsCdna())); + setScaleProteinAsCdna(applet.getDefaultParameter("scaleProteinAsCdna", + isScaleProteinAsCdna())); String param = applet.getParameter("upperCase"); if (param != null) @@ -190,9 +184,9 @@ public class AlignViewport extends AlignmentViewport implements if (applet != null) { - String colour = al.isNucleotide() ? applet - .getParameter("defaultColourNuc") : applet - .getParameter("defaultColourProt"); + String colour = al.isNucleotide() + ? applet.getParameter("defaultColourNuc") + : applet.getParameter("defaultColourProt"); if (colour == null) { colour = applet.getParameter("defaultColour"); @@ -208,68 +202,29 @@ public class AlignViewport extends AlignmentViewport implements if (colour != null) { - globalColourScheme = ColourSchemeProperty.getColourScheme( - alignment, colour); - if (globalColourScheme != null) + residueShading = new ResidueShader( + ColourSchemeProperty.getColourScheme(this, alignment, + colour)); + if (residueShading != null) { - globalColourScheme.setConsensus(hconsensus); + residueShading.setConsensus(consensusProfiles); } } if (applet.getParameter("userDefinedColour") != null) { - ((UserColourScheme) globalColourScheme).parseAppletParameter(applet - .getParameter("userDefinedColour")); + residueShading = new ResidueShader(new UserColourScheme( + applet.getParameter("userDefinedColour"))); } } initAutoAnnotation(); - } /** - * get the consensus sequence as displayed under the PID consensus annotation - * row. - * - * @return consensus sequence as a new sequence object + * {@inheritDoc} */ - public SequenceI getConsensusSeq() - { - if (consensus == null) - { - updateConsensus(null); - } - if (consensus == null) - { - return null; - } - StringBuilder seqs = new StringBuilder(consensus.annotations.length); - for (int i = 0; i < consensus.annotations.length; i++) - { - if (consensus.annotations[i] != null) - { - if (consensus.annotations[i].description.charAt(0) == '[') - { - seqs.append(consensus.annotations[i].description.charAt(1)); - } - else - { - seqs.append(consensus.annotations[i].displayCharacter); - } - } - } - SequenceI sq = new Sequence("Consensus", seqs.toString()); - sq.setDescription("Percentage Identity Consensus " - + ((ignoreGapsInConsensusCalculation) ? " without gaps" : "")); - return sq; - } - - java.awt.Frame nullFrame; - - protected FeatureSettings featureSettings = null; - - private float heightScale = 1, widthScale = 1; - - public void setFont(Font f) + @Override + public void setFont(Font f, boolean setGrid) { font = f; if (nullFrame == null) @@ -278,15 +233,19 @@ 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); - setCharWidth((int) (widthScale * (fm.stringWidth("MMMMMMMMMMM") / 10))); + FontMetrics fm = nullFrame.getGraphics().getFontMetrics(f2); + setCharWidth( + (int) (widthScale * (fm.stringWidth("MMMMMMMMMMM") / 10))); } } @@ -297,17 +256,7 @@ public class AlignViewport extends AlignmentViewport implements public void resetSeqLimits(int height) { - setEndSeq(height / getCharHeight()); - } - - public void setCurrentTree(NJTree tree) - { - currentTree = tree; - } - - public NJTree getCurrentTree() - { - return currentTree; + ranges.setEndSeq(height / getCharHeight()); } boolean centreColumnLabels; @@ -333,7 +282,8 @@ public class AlignViewport extends AlignmentViewport implements { getStructureSelectionManager().sendSelection( new SequenceGroup(getSelectionGroup()), - new ColumnSelection(getColumnSelection()), this); + new ColumnSelection(getColumnSelection()), + new HiddenColumns(getAlignment().getHiddenColumns()), this); } /** @@ -349,17 +299,6 @@ public class AlignViewport extends AlignmentViewport implements .getStructureSelectionManager(applet); } - @Override - public boolean isNormaliseSequenceLogo() - { - return normaliseSequenceLogo; - } - - public void setNormaliseSequenceLogo(boolean state) - { - normaliseSequenceLogo = state; - } - /** * * @return true if alignment characters should be displayed @@ -438,8 +377,9 @@ public class AlignViewport extends AlignmentViewport implements int seqOffset = findComplementScrollTarget(sr); if (!sr.isEmpty()) { - complementPanel.setFollowingComplementScroll(true); + complementPanel.setToScrollComplementPanel(false); complementPanel.scrollToCentre(sr, seqOffset); + complementPanel.setToScrollComplementPanel(true); } }