X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=ef09b976e4b4b6979f50e146be3947770d25fb3a;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=1767164dc2af7ebed5e8e801735c6396942869ed;hpb=1d4b37e9bd54c095aa00e643b741c931eb61c58b;p=jalview.git diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java index 1767164..ef09b97 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 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -23,81 +23,38 @@ package jalview.appletgui; import jalview.analysis.NJTree; import jalview.api.AlignViewportI; import jalview.bin.JalviewLite; +import jalview.commands.CommandI; import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; +import jalview.datamodel.SearchResults; import jalview.datamodel.Sequence; 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.viewmodel.AlignmentViewport; import java.awt.Font; -import java.util.Stack; public class AlignViewport extends AlignmentViewport implements - AlignViewportI, SelectionSource, VamsasSource + SelectionSource, VamsasSource, CommandListener { - 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; - public jalview.bin.JalviewLite applet; boolean MAC = false; - Stack historyList = new Stack(); - - Stack redoList = new Stack(); - private AnnotationColumnChooser annotationColumnSelectionState; public void finalize() @@ -110,9 +67,10 @@ 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; // we always pad gaps this.setPadGaps(true); this.startRes = 0; @@ -138,7 +96,7 @@ 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 +119,7 @@ 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 +133,11 @@ 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 +147,25 @@ 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 +187,13 @@ 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"); @@ -272,7 +239,7 @@ 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 +260,6 @@ 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 +277,13 @@ 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))); } } @@ -383,99 +292,6 @@ 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()); @@ -491,78 +307,6 @@ public class AlignViewport extends AlignmentViewport implements 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 +314,6 @@ public class AlignViewport extends AlignmentViewport implements return centreColumnLabels; } - public boolean followHighlight = true; - - public boolean getFollowHighlight() - { - return followHighlight; - } - public boolean followSelection = true; /** @@ -590,10 +327,22 @@ public class AlignViewport extends AlignmentViewport implements 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); + } + + /** + * Returns an instance of the StructureSelectionManager scoped to this applet + * instance. + * + * @return + */ + @Override + public StructureSelectionManager getStructureSelectionManager() + { + return jalview.structure.StructureSelectionManager + .getStructureSelectionManager(applet); } /** @@ -629,12 +378,6 @@ public class AlignViewport extends AlignmentViewport implements } } - @Override - public boolean hasHiddenColumns() - { - return hasHiddenColumns; - } - public boolean isNormaliseSequenceLogo() { return normaliseSequenceLogo; @@ -665,4 +408,66 @@ 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. + */ + SearchResults sr = new SearchResults(); + int seqOffset = findComplementScrollTarget(sr); + if (!sr.isEmpty()) + { + complementPanel.setFollowingComplementScroll(true); + complementPanel.scrollToCentre(sr, seqOffset); + } + } + }