From 0b9d0f8eba1cec46c0b31fdd402a826e26244ff5 Mon Sep 17 00:00:00 2001 From: jprocter Date: Wed, 30 May 2012 19:30:41 +0100 Subject: [PATCH] JAL-969 - refactor colourscheme machinery from GUI code to core alignment view model --- src/jalview/appletgui/AlignFrame.java | 62 ---------------- src/jalview/appletgui/AlignViewport.java | 35 --------- src/jalview/gui/AlignFrame.java | 2 +- src/jalview/gui/AlignViewport.java | 116 ------------------------------ src/jalview/gui/TextColourChooser.java | 6 +- 5 files changed, 4 insertions(+), 217 deletions(-) diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index 6ce68c3..fce736f 100644 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -2346,68 +2346,6 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, ItemLis } viewport.setGlobalColourScheme(cs); - if (viewport.getColourAppliesToAllGroups()) - { - Vector groups = viewport.getAlignment().getGroups(); - for (int i = 0; i < groups.size(); i++) - { - SequenceGroup sg = (SequenceGroup) groups.elementAt(i); - - if (cs == null) - { - sg.cs = null; - continue; - } - if (cs instanceof ClustalxColourScheme) - { - sg.cs = new ClustalxColourScheme( - sg.getSequences(viewport.getHiddenRepSequences()), - sg.getWidth()); - } - else - { - try - { - sg.cs = cs.getClass().newInstance(); - } catch (Exception ex) - { - ex.printStackTrace(); - sg.cs = cs; - } - } - - if (viewport.getAbovePIDThreshold() - || cs instanceof PIDColourScheme - || cs instanceof Blosum62ColourScheme) - { - sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus()); - sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(viewport.getHiddenRepSequences()), 0, - sg.getWidth())); - } - else - { - sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus()); - } - - if (viewport.getConservationSelected()) - { - Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, - sg.getSequences(viewport.getHiddenRepSequences()), 0, - viewport.getAlignment().getWidth() - 1); - c.calculate(); - c.verdict(false, viewport.getConsPercGaps()); - sg.cs.setConservation(c); - } - else - { - sg.cs.setConservation(null); - sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus()); - } - - } - } if (alignPanel.getOverviewPanel() != null) { diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java index 9258e3a..e0a6a71 100644 --- a/src/jalview/appletgui/AlignViewport.java +++ b/src/jalview/appletgui/AlignViewport.java @@ -63,11 +63,6 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI, boolean upperCasebold = false; - boolean colourAppliesToAllGroups = true; - - boolean conservationColourSelected = false; - - boolean abovePIDThreshold = false; int charHeight; @@ -300,26 +295,6 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI, return sq; } - public boolean getConservationSelected() - { - return conservationColourSelected; - } - - public void setConservationSelected(boolean b) - { - conservationColourSelected = b; - } - - public boolean getAbovePIDThreshold() - { - return abovePIDThreshold; - } - - public void setAbovePIDThreshold(boolean b) - { - abovePIDThreshold = b; - } - public int getStartRes() { return startRes; @@ -538,16 +513,6 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI, return currentTree; } - public void setColourAppliesToAllGroups(boolean b) - { - colourAppliesToAllGroups = b; - } - - public boolean getColourAppliesToAllGroups() - { - return colourAppliesToAllGroups; - } - public boolean getShowJVSuffix() { return showJVSuffix; diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 76001a5..3a0e3f5 100755 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -718,7 +718,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, showSeqFeatures.setSelected(av.showSequenceFeatures); hiddenMarkers.setState(av.showHiddenMarkers); - applyToAllGroups.setState(av.colourAppliesToAllGroups); + applyToAllGroups.setState(av.getColourAppliesToAllGroups()); showNpFeatsMenuitem.setSelected(av.isShowNpFeats()); showDbRefsMenuitem.setSelected(av.isShowDbRefs()); autoCalculate.setSelected(av.autoCalculateConsensus); diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index 8bb40a1..7294bae 100644 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -93,12 +93,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource, boolean showAnnotation = true; - boolean colourAppliesToAllGroups = true; - - boolean conservationColourSelected = false; - - boolean abovePIDThreshold = false; - int charHeight; int charWidth; @@ -111,9 +105,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource, boolean seqNameItalics; - int threshold; - - int increment; NJTree currentTree = null; @@ -437,50 +428,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource, return sq; } - - /** - * GUI state - * - * @return true if conservation based shading is enabled - */ - public boolean getConservationSelected() - { - return conservationColourSelected; - } - - /** - * GUI state - * - * @param b - * enable conservation based shading - */ - public void setConservationSelected(boolean b) - { - conservationColourSelected = b; - } - - /** - * GUI state - * - * @return true if percent identity threshold is applied to shading - */ - public boolean getAbovePIDThreshold() - { - return abovePIDThreshold; - } - - /** - * GUI state - * - * - * @param b - * indicate if percent identity threshold is applied to shading - */ - public void setAbovePIDThreshold(boolean b) - { - abovePIDThreshold = b; - } - /** * DOCUMENT ME! * @@ -831,48 +778,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource, /** * DOCUMENT ME! * - * @param thresh - * DOCUMENT ME! - */ - public void setThreshold(int thresh) - { - threshold = thresh; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getThreshold() - { - return threshold; - } - - /** - * DOCUMENT ME! - * - * @param inc - * DOCUMENT ME! - */ - public void setIncrement(int inc) - { - increment = inc; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getIncrement() - { - return increment; - } - - /** - * DOCUMENT ME! - * * @return DOCUMENT ME! */ public ColumnSelection getColumnSelection() @@ -904,27 +809,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource, /** * DOCUMENT ME! * - * @param b - * DOCUMENT ME! - */ - public void setColourAppliesToAllGroups(boolean b) - { - colourAppliesToAllGroups = b; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getColourAppliesToAllGroups() - { - return colourAppliesToAllGroups; - } - - /** - * DOCUMENT ME! - * * @return DOCUMENT ME! */ public boolean getShowJVSuffix() diff --git a/src/jalview/gui/TextColourChooser.java b/src/jalview/gui/TextColourChooser.java index 1627ab7..614bfee 100644 --- a/src/jalview/gui/TextColourChooser.java +++ b/src/jalview/gui/TextColourChooser.java @@ -137,7 +137,7 @@ public class TextColourChooser if (sg == null) { ap.av.textColour = col; - if (ap.av.colourAppliesToAllGroups) + if (ap.av.getColourAppliesToAllGroups()) { setGroupTextColour(); } @@ -155,7 +155,7 @@ public class TextColourChooser if (sg == null) { ap.av.textColour2 = col; - if (ap.av.colourAppliesToAllGroups) + if (ap.av.getColourAppliesToAllGroups()) { setGroupTextColour(); } @@ -173,7 +173,7 @@ public class TextColourChooser if (sg == null) { ap.av.thresholdTextColour = value; - if (ap.av.colourAppliesToAllGroups) + if (ap.av.getColourAppliesToAllGroups()) { setGroupTextColour(); } -- 1.7.10.2