From 4f094851cd2247ea2d982e7829a6f5b663042573 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Tue, 31 Jan 2017 14:40:51 +0000 Subject: [PATCH] JAL-2371 rename global/viewportColourScheme to residueShading --- src/jalview/api/AlignViewportI.java | 2 +- src/jalview/appletgui/AlignFrame.java | 4 +-- src/jalview/appletgui/AlignViewport.java | 8 ++--- src/jalview/appletgui/SeqPanel.java | 4 +-- src/jalview/appletgui/SequenceRenderer.java | 6 ++-- src/jalview/appletgui/TreeCanvas.java | 4 +-- src/jalview/appletgui/UserDefinedColours.java | 2 +- src/jalview/gui/AlignFrame.java | 12 +++---- src/jalview/gui/AlignViewport.java | 14 ++++----- src/jalview/gui/Jalview2XML.java | 8 ++--- src/jalview/gui/Jalview2XML_V1.java | 6 ++-- src/jalview/gui/SeqPanel.java | 4 +-- src/jalview/gui/SequenceRenderer.java | 8 ++--- src/jalview/gui/TreeCanvas.java | 4 +-- src/jalview/renderer/AnnotationRenderer.java | 2 +- src/jalview/viewmodel/AlignmentViewport.java | 26 +++++++-------- src/jalview/workers/ConsensusThread.java | 2 +- test/jalview/gui/AlignFrameTest.java | 42 ++++++++++++------------- test/jalview/gui/AlignViewportTest.java | 2 +- test/jalview/io/Jalview2xmlTests.java | 4 +-- test/jalview/schemes/PIDColourSchemeTest.java | 4 +-- 21 files changed, 84 insertions(+), 84 deletions(-) diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java index 33a0061..2802684 100644 --- a/src/jalview/api/AlignViewportI.java +++ b/src/jalview/api/AlignViewportI.java @@ -86,7 +86,7 @@ public interface AlignViewportI extends ViewStyleI * * @return */ - ResidueShaderI getViewportColourScheme(); + ResidueShaderI getResidueShading(); AlignmentI getAlignment(); diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index d30f10d..5cabda3 100644 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -2642,7 +2642,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, && viewport.getGlobalColourScheme() != null) { SliderPanel.setPIDSliderSource(alignPanel, - viewport.getViewportColourScheme(), alignPanel.getViewName()); + viewport.getResidueShading(), alignPanel.getViewName()); SliderPanel.showPIDSlider(); } } @@ -2653,7 +2653,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, && viewport.getGlobalColourScheme() != null) { SliderPanel.setConservationSlider(alignPanel, - viewport.getViewportColourScheme(), alignPanel.getViewName()); + viewport.getResidueShading(), alignPanel.getViewName()); SliderPanel.showConservationSlider(); } } diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java index 29df968..fc087c6 100644 --- a/src/jalview/appletgui/AlignViewport.java +++ b/src/jalview/appletgui/AlignViewport.java @@ -209,17 +209,17 @@ public class AlignViewport extends AlignmentViewport implements if (colour != null) { - globalColourScheme = new ResidueShader( + residueShading = new ResidueShader( ColourSchemeProperty.getColourScheme(alignment, colour)); - if (globalColourScheme != null) + if (residueShading != null) { - globalColourScheme.setConsensus(hconsensus); + residueShading.setConsensus(hconsensus); } } if (applet.getParameter("userDefinedColour") != null) { - globalColourScheme = new ResidueShader( + residueShading = new ResidueShader( new UserColourScheme( applet.getParameter("userDefinedColour"))); } diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java index 41529cd..8cfd2dc 100644 --- a/src/jalview/appletgui/SeqPanel.java +++ b/src/jalview/appletgui/SeqPanel.java @@ -1505,12 +1505,12 @@ public class SeqPanel extends Panel implements MouseMotionListener, if (av.getConservationSelected()) { - SliderPanel.setConservationSlider(ap, av.getViewportColourScheme(), + SliderPanel.setConservationSlider(ap, av.getResidueShading(), ap.getViewName()); } if (av.getAbovePIDThreshold()) { - SliderPanel.setPIDSliderSource(ap, av.getViewportColourScheme(), + SliderPanel.setPIDSliderSource(ap, av.getResidueShading(), ap.getViewName()); } diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java index 1c7c4ce..86d1f98 100755 --- a/src/jalview/appletgui/SequenceRenderer.java +++ b/src/jalview/appletgui/SequenceRenderer.java @@ -83,7 +83,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer } else if (av.getShowBoxes()) { - getBoxColour(av.getViewportColourScheme(), seq, i); + getBoxColour(av.getResidueShading(), seq, i); } return resBoxColour; @@ -182,7 +182,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer } else if (av.getShowBoxes()) { - getBoxColour(av.getViewportColourScheme(), seq, i); + getBoxColour(av.getResidueShading(), seq, i); } } @@ -272,7 +272,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer if (av.getColourText()) { - getBoxColour(av.getViewportColourScheme(), seq, i); + getBoxColour(av.getResidueShading(), seq, i); if (av.getShowBoxes()) { graphics.setColor(resBoxColour.darker()); diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java index 510df94..e30879c 100755 --- a/src/jalview/appletgui/TreeCanvas.java +++ b/src/jalview/appletgui/TreeCanvas.java @@ -672,13 +672,13 @@ public class TreeCanvas extends Panel implements MouseListener, // instead we set it manually - recalc called after updateAnnotation sg.setColourScheme(cs); sg.getGroupColourScheme().setThreshold( - av.getViewportColourScheme().getThreshold(), + av.getResidueShading().getThreshold(), av.isIgnoreGapsConsensus()); sg.setName("JTreeGroup:" + sg.hashCode()); sg.setIdColour(col); if (av.getGlobalColourScheme() != null - && av.getViewportColourScheme().conservationApplied()) + && av.getResidueShading().conservationApplied()) { Conservation c = new Conservation("Group", sg.getSequences(null), sg.getStartRes(), sg.getEndRes()); diff --git a/src/jalview/appletgui/UserDefinedColours.java b/src/jalview/appletgui/UserDefinedColours.java index b794724..95e36b5 100644 --- a/src/jalview/appletgui/UserDefinedColours.java +++ b/src/jalview/appletgui/UserDefinedColours.java @@ -513,7 +513,7 @@ public class UserDefinedColours extends Panel implements ActionListener, else { ap.av.setGlobalColourScheme(ucs); - ap.av.getViewportColourScheme().setThreshold(0, + ap.av.getResidueShading().setThreshold(0, ap.av.isIgnoreGapsConsensus()); } ap.seqPanel.seqCanvas.img = null; diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index cf6a901..b5fc817 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -3359,7 +3359,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void modifyPID_actionPerformed() { SliderPanel.setPIDSliderSource(alignPanel, - viewport.getViewportColourScheme(), alignPanel.getViewName()); + viewport.getResidueShading(), alignPanel.getViewName()); SliderPanel.showPIDSlider(); } @@ -3370,7 +3370,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void modifyConservation_actionPerformed() { SliderPanel.setConservationSlider(alignPanel, - viewport.getViewportColourScheme(), alignPanel.getViewName()); + viewport.getResidueShading(), alignPanel.getViewName()); SliderPanel.showConservationSlider(); } @@ -3382,7 +3382,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { modifyConservation.setEnabled(selected); viewport.setConservationSelected(selected); - viewport.getViewportColourScheme().setConservationApplied(selected); + viewport.getResidueShading().setConservationApplied(selected); changeColour(viewport.getGlobalColourScheme()); if (selected) @@ -3405,7 +3405,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.setAbovePIDThreshold(selected); if (!selected) { - viewport.getViewportColourScheme().setThreshold(0, + viewport.getResidueShading().setThreshold(0, viewport.isIgnoreGapsConsensus()); } @@ -4838,7 +4838,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (viewport.getConservationSelected()) { SliderPanel.setConservationSlider(alignPanel, - viewport.getViewportColourScheme(), alignPanel.getViewName()); + viewport.getResidueShading(), alignPanel.getViewName()); } else { @@ -4847,7 +4847,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (viewport.getAbovePIDThreshold()) { SliderPanel.setPIDSliderSource(alignPanel, - viewport.getViewportColourScheme(), alignPanel.getViewName()); + viewport.getResidueShading(), alignPanel.getViewName()); } else { diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index ea9eb21..69f155b 100644 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -295,18 +295,18 @@ public class AlignViewport extends AlignmentViewport implements { ColourSchemeI colourScheme = ColourSchemeProperty.getColourScheme( alignment, propertyValue); - globalColourScheme = new ResidueShader(colourScheme); + residueShading = new ResidueShader(colourScheme); if (colourScheme instanceof UserColourScheme) { - globalColourScheme = new ResidueShader( + residueShading = new ResidueShader( UserDefinedColours.loadDefaultColours()); - globalColourScheme.setThreshold(0, isIgnoreGapsConsensus()); + residueShading.setThreshold(0, isIgnoreGapsConsensus()); } - if (globalColourScheme != null) + if (residueShading != null) { - globalColourScheme.setConsensus(hconsensus); + residueShading.setConsensus(hconsensus); } } } @@ -385,9 +385,9 @@ public class AlignViewport extends AlignmentViewport implements super.setViewStyle(settingsForView); setFont(new Font(viewStyle.getFontName(), viewStyle.getFontStyle(), viewStyle.getFontSize()), false); - if (globalColourScheme != null) + if (residueShading != null) { - globalColourScheme.setConservationApplied(settingsForView + residueShading.setConservationApplied(settingsForView .isConservationColourSelected()); } } diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index d5ec6ac..3ac453f 100644 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -1294,7 +1294,7 @@ public class Jalview2XML .getGlobalColourScheme())); } - ResidueShaderI vcs = av.getViewportColourScheme(); + ResidueShaderI vcs = av.getResidueShading(); ColourSchemeI cs = av.getGlobalColourScheme(); if (cs != null) @@ -4474,15 +4474,15 @@ public class Jalview2XML } af.viewport.setGlobalColourScheme(cs); - af.viewport.getViewportColourScheme().setThreshold( + af.viewport.getResidueShading().setThreshold( view.getPidThreshold(), true); - af.viewport.getViewportColourScheme().setConsensus( + af.viewport.getResidueShading().setConsensus( af.viewport.getSequenceConsensusHash()); af.viewport.setColourAppliesToAllGroups(false); if (view.getConservationSelected() && cs != null) { - af.viewport.getViewportColourScheme().setConservationInc( + af.viewport.getResidueShading().setConservationInc( view.getConsThreshold()); } diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java index 7472877..e751a2c 100755 --- a/src/jalview/gui/Jalview2XML_V1.java +++ b/src/jalview/gui/Jalview2XML_V1.java @@ -405,16 +405,16 @@ public class Jalview2XML_V1 // } } - af.viewport.getViewportColourScheme().setThreshold( + af.viewport.getResidueShading().setThreshold( view.getPidThreshold(), true); - af.viewport.getViewportColourScheme().setConsensus( + af.viewport.getResidueShading().setConsensus( af.viewport.getSequenceConsensusHash()); af.viewport.setColourAppliesToAllGroups(false); af.alignPanel.updateLayout(); af.changeColour(cs); if (view.getConservationSelected() && cs != null) { - af.viewport.getViewportColourScheme().setConservationInc( + af.viewport.getResidueShading().setConservationInc( view.getConsThreshold()); } diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 6214a7c..e402d28 100644 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -1655,13 +1655,13 @@ public class SeqPanel extends JPanel implements MouseListener, if (av.getConservationSelected()) { - SliderPanel.setConservationSlider(ap, av.getViewportColourScheme(), + SliderPanel.setConservationSlider(ap, av.getResidueShading(), ap.getViewName()); } if (av.getAbovePIDThreshold()) { - SliderPanel.setPIDSliderSource(ap, av.getViewportColourScheme(), + SliderPanel.setPIDSliderSource(ap, av.getResidueShading(), ap.getViewName()); } if ((stretchGroup != null) && (stretchGroup.getEndRes() == res)) diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java index e77536d..95c3261 100755 --- a/src/jalview/gui/SequenceRenderer.java +++ b/src/jalview/gui/SequenceRenderer.java @@ -98,7 +98,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer } else if (av.getShowBoxes()) { - getBoxColour(av.getViewportColourScheme(), seq, i); + getBoxColour(av.getResidueShading(), seq, i); } return resBoxColour; @@ -241,7 +241,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer } else if (av.getShowBoxes()) { - getBoxColour(av.getViewportColourScheme(), seq, i); + getBoxColour(av.getResidueShading(), seq, i); } } @@ -387,7 +387,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer if (av.getColourText()) { getboxColour = true; - getBoxColour(av.getViewportColourScheme(), seq, i); + getBoxColour(av.getResidueShading(), seq, i); if (av.getShowBoxes()) { @@ -403,7 +403,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer { if (!getboxColour) { - getBoxColour(av.getViewportColourScheme(), seq, i); + getBoxColour(av.getResidueShading(), seq, i); } if (resBoxColour.getRed() + resBoxColour.getBlue() diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java index 9fa98ee..54eed1a 100755 --- a/src/jalview/gui/TreeCanvas.java +++ b/src/jalview/gui/TreeCanvas.java @@ -1010,7 +1010,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } sg.setColourScheme(cs); sg.getGroupColourScheme().setThreshold( - av.getViewportColourScheme().getThreshold(), + av.getResidueShading().getThreshold(), av.isIgnoreGapsConsensus()); // sg.recalcConservation(); sg.setName("JTreeGroup:" + sg.hashCode()); @@ -1019,7 +1019,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, for (int a = 0; a < aps.length; a++) { if (aps[a].av.getGlobalColourScheme() != null - && aps[a].av.getViewportColourScheme() + && aps[a].av.getResidueShading() .conservationApplied()) { Conservation c = new Conservation("Group", sg.getSequences(null), diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java index 9b0d938..6f84a2e 100644 --- a/src/jalview/renderer/AnnotationRenderer.java +++ b/src/jalview/renderer/AnnotationRenderer.java @@ -314,7 +314,7 @@ public class AnnotationRenderer av_renderHistogram = av.isShowConsensusHistogram(); av_renderProfile = av.isShowSequenceLogo(); av_normaliseProfile = av.isNormaliseSequenceLogo(); - profcolour = av.getViewportColourScheme(); + profcolour = av.getResidueShading(); if (profcolour == null || profcolour.getColourScheme() == null) { /* diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java index 544835d..abb8f63 100644 --- a/src/jalview/viewmodel/AlignmentViewport.java +++ b/src/jalview/viewmodel/AlignmentViewport.java @@ -597,7 +597,7 @@ public abstract class AlignmentViewport implements AlignViewportI, protected boolean ignoreGapsInConsensusCalculation = false; - protected ResidueShaderI globalColourScheme; + protected ResidueShaderI residueShading; @Override public void setGlobalColourScheme(ColourSchemeI cs) @@ -615,11 +615,11 @@ public abstract class AlignmentViewport implements AlignViewportI, * this means that any conservation or PID threshold settings * persist when the alignment colour scheme is changed */ - if (globalColourScheme == null) + if (residueShading == null) { - globalColourScheme = new ResidueShader(viewStyle); + residueShading = new ResidueShader(viewStyle); } - globalColourScheme.setColourScheme(cs); + residueShading.setColourScheme(cs); // TODO: do threshold and increment belong in ViewStyle or ResidueShader? // ...problem: groups need these, but do not currently have a ViewStyle @@ -631,9 +631,9 @@ public abstract class AlignmentViewport implements AlignViewportI, // || cs instanceof Blosum62ColourScheme) if (getConservationSelected()) { - globalColourScheme.setConservation(hconservation); + residueShading.setConservation(hconservation); } - globalColourScheme.alignmentChanged(alignment, hiddenRepSequences); + residueShading.alignmentChanged(alignment, hiddenRepSequences); } /* @@ -661,14 +661,14 @@ public abstract class AlignmentViewport implements AlignViewportI, @Override public ColourSchemeI getGlobalColourScheme() { - return globalColourScheme == null ? null : globalColourScheme + return residueShading == null ? null : residueShading .getColourScheme(); } @Override - public ResidueShaderI getViewportColourScheme() + public ResidueShaderI getResidueShading() { - return globalColourScheme; + return residueShading; } protected AlignmentAnnotation consensus; @@ -928,7 +928,7 @@ public abstract class AlignmentViewport implements AlignViewportI, hconsensus = null; hcomplementConsensus = null; // colour scheme may hold reference to consensus - globalColourScheme = null; + residueShading = null; // TODO remove listeners from changeSupport? changeSupport = null; setAlignment(null); @@ -1198,9 +1198,9 @@ public abstract class AlignmentViewport implements AlignViewportI, if (ap != null) { updateConsensus(ap); - if (globalColourScheme != null) + if (residueShading != null) { - globalColourScheme.setThreshold(globalColourScheme.getThreshold(), + residueShading.setThreshold(residueShading.getThreshold(), ignoreGapsInConsensusCalculation); } } @@ -1846,7 +1846,7 @@ public abstract class AlignmentViewport implements AlignViewportI, */ void updateAllColourSchemes() { - ResidueShaderI rs = globalColourScheme; + ResidueShaderI rs = residueShading; if (rs != null) { rs.alignmentChanged(alignment, hiddenRepSequences); diff --git a/src/jalview/workers/ConsensusThread.java b/src/jalview/workers/ConsensusThread.java index fa3fe75..0c7e69a 100644 --- a/src/jalview/workers/ConsensusThread.java +++ b/src/jalview/workers/ConsensusThread.java @@ -147,7 +147,7 @@ public class ConsensusThread extends AlignCalcWorker */ protected void setColourSchemeConsensus(ProfilesI hconsensus) { - ResidueShaderI cs = alignViewport.getViewportColourScheme(); + ResidueShaderI cs = alignViewport.getResidueShading(); if (cs != null) { cs.setConsensus(hconsensus); diff --git a/test/jalview/gui/AlignFrameTest.java b/test/jalview/gui/AlignFrameTest.java index 8ba165e..2ea94a4 100644 --- a/test/jalview/gui/AlignFrameTest.java +++ b/test/jalview/gui/AlignFrameTest.java @@ -183,8 +183,8 @@ public class AlignFrameTest af.applyToAllGroups_actionPerformed(false); af.changeColour_actionPerformed(JalviewColourScheme.Buried.toString()); assertTrue(av.getGlobalColourScheme() instanceof BuriedColourScheme); - assertFalse(av.getViewportColourScheme().conservationApplied()); - assertEquals(av.getViewportColourScheme().getThreshold(), 0); + assertFalse(av.getResidueShading().conservationApplied()); + assertEquals(av.getResidueShading().getThreshold(), 0); /* * Apply Conservation 20% @@ -196,8 +196,8 @@ public class AlignFrameTest new String[] { "Background" })); assertTrue(sp.isForConservation()); sp.valueChanged(20); - assertTrue(av.getViewportColourScheme().conservationApplied()); - assertEquals(av.getViewportColourScheme().getConservationInc(), 20); + assertTrue(av.getResidueShading().conservationApplied()); + assertEquals(av.getResidueShading().getConservationInc(), 20); /* * Apply PID threshold 10% (conservation still applies as well) @@ -209,9 +209,9 @@ public class AlignFrameTest "label.percentage_identity_threshold", new String[] { "Background" })); sp.valueChanged(10); - assertEquals(av.getViewportColourScheme().getThreshold(), 10); - assertTrue(av.getViewportColourScheme().conservationApplied()); - assertEquals(av.getViewportColourScheme().getConservationInc(), 20); + assertEquals(av.getResidueShading().getThreshold(), 10); + assertTrue(av.getResidueShading().conservationApplied()); + assertEquals(av.getResidueShading().getConservationInc(), 20); /* * create a group with Strand colouring, 30% Conservation @@ -263,9 +263,9 @@ public class AlignFrameTest */ af.changeColour_actionPerformed(JalviewColourScheme.Turn.toString()); assertTrue(av.getGlobalColourScheme() instanceof TurnColourScheme); - assertTrue(av.getViewportColourScheme().conservationApplied()); - assertEquals(av.getViewportColourScheme().getConservationInc(), 20); - assertEquals(av.getViewportColourScheme().getThreshold(), 10); + assertTrue(av.getResidueShading().conservationApplied()); + assertEquals(av.getResidueShading().getConservationInc(), 20); + assertEquals(av.getResidueShading().getThreshold(), 10); assertTrue(sg.getColourScheme() instanceof StrandColourScheme); assertTrue(sg.getGroupColourScheme().conservationApplied()); assertEquals(sg.getGroupColourScheme().getConservationInc(), 30); @@ -278,9 +278,9 @@ public class AlignFrameTest af.applyToAllGroups_actionPerformed(true); af.changeColour_actionPerformed(JalviewColourScheme.Helix.toString()); assertTrue(av.getGlobalColourScheme() instanceof HelixColourScheme); - assertTrue(av.getViewportColourScheme().conservationApplied()); - assertEquals(av.getViewportColourScheme().getConservationInc(), 20); - assertEquals(av.getViewportColourScheme().getThreshold(), 10); + assertTrue(av.getResidueShading().conservationApplied()); + assertEquals(av.getResidueShading().getConservationInc(), 20); + assertEquals(av.getResidueShading().getThreshold(), 10); assertTrue(sg.getColourScheme() instanceof HelixColourScheme); assertTrue(sg.getGroupColourScheme().conservationApplied()); assertEquals(sg.getGroupColourScheme().getConservationInc(), 30); @@ -314,8 +314,8 @@ public class AlignFrameTest af.applyToAllGroups_actionPerformed(false); af.changeColour_actionPerformed(JalviewColourScheme.Helix.toString()); assertTrue(av.getGlobalColourScheme() instanceof HelixColourScheme); - assertFalse(av.getViewportColourScheme().conservationApplied()); - assertEquals(av.getViewportColourScheme().getThreshold(), 0); + assertFalse(av.getResidueShading().conservationApplied()); + assertEquals(av.getResidueShading().getThreshold(), 0); /* * inspect the colour of @@ -323,7 +323,7 @@ public class AlignFrameTest * FER_CAPAN.10(SER), column 16 (15 base 0) */ SequenceI ferCapan = al.findName("FER_CAPAN"); - ResidueShaderI rs = av.getViewportColourScheme(); + ResidueShaderI rs = av.getResidueShading(); Color c = rs.findColour('I', 14, ferCapan); Color i_original = new Color(138, 117, 138); assertEquals(c, i_original); @@ -339,7 +339,7 @@ public class AlignFrameTest assertTrue(sp.isForConservation()); assertEquals(sp.getValue(), 30); // initial slider setting sp.valueChanged(10); - assertSame(rs, av.getViewportColourScheme()); + assertSame(rs, av.getResidueShading()); c = rs.findColour('I', 14, ferCapan); Color i_faded = new Color(196, 186, 196); assertEquals(c, i_faded); @@ -490,7 +490,7 @@ public class AlignFrameTest sp = SliderPanel.getSliderPanel(); assertTrue(sp.isForConservation()); sp.valueChanged(20); - ResidueShaderI rs = av.getViewportColourScheme(); + ResidueShaderI rs = av.getResidueShading(); assertEquals(rs.getThreshold(), 10); assertTrue(rs.conservationApplied()); assertEquals(rs.getConservationInc(), 20); @@ -540,8 +540,8 @@ public class AlignFrameTest assertEquals(af.alignPanel.getViewName(), "View 1"); AlignViewport av2 = af.getViewport(); assertNotSame(av, av2); - rs = av2.getViewportColourScheme(); - assertNotSame(av.getViewportColourScheme(), rs); + rs = av2.getResidueShading(); + assertNotSame(av.getResidueShading(), rs); assertEquals(rs.getThreshold(), 10); assertTrue(rs.conservationApplied()); assertEquals(rs.getConservationInc(), 20); @@ -562,6 +562,6 @@ public class AlignFrameTest "label.conservation_colour_increment", new String[] { "View 1" })); sp.valueChanged(22); - assertEquals(av2.getViewportColourScheme().getConservationInc(), 22); + assertEquals(av2.getResidueShading().getConservationInc(), 22); } } diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java index 71a5f3c..1cdcdb7 100644 --- a/test/jalview/gui/AlignViewportTest.java +++ b/test/jalview/gui/AlignViewportTest.java @@ -355,7 +355,7 @@ public class AlignViewportTest "examples/uniref50.fa", DataSourceType.FILE); ColourSchemeI cs = new PIDColourScheme(); af.getViewport().setGlobalColourScheme(cs); - assertFalse(af.getViewport().getViewportColourScheme() + assertFalse(af.getViewport().getResidueShading() .conservationApplied()); } diff --git a/test/jalview/io/Jalview2xmlTests.java b/test/jalview/io/Jalview2xmlTests.java index af52c55..6abb7e5 100644 --- a/test/jalview/io/Jalview2xmlTests.java +++ b/test/jalview/io/Jalview2xmlTests.java @@ -777,7 +777,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase sp = SliderPanel.getSliderPanel(); assertTrue(sp.isForConservation()); sp.valueChanged(20); - ResidueShaderI rs = av.getViewportColourScheme(); + ResidueShaderI rs = av.getResidueShading(); assertEquals(rs.getThreshold(), 10); assertTrue(rs.conservationApplied()); assertEquals(rs.getConservationInc(), 20); @@ -824,7 +824,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase /* * verify alignment (background) colouring */ - rs = af.getViewport().getViewportColourScheme(); + rs = af.getViewport().getResidueShading(); assertTrue(rs.getColourScheme() instanceof BuriedColourScheme); assertEquals(rs.getThreshold(), 10); assertTrue(rs.conservationApplied()); diff --git a/test/jalview/schemes/PIDColourSchemeTest.java b/test/jalview/schemes/PIDColourSchemeTest.java index 8bab428..73b270f 100644 --- a/test/jalview/schemes/PIDColourSchemeTest.java +++ b/test/jalview/schemes/PIDColourSchemeTest.java @@ -90,7 +90,7 @@ public class PIDColourSchemeTest * including gaps, A should be coloured for 50% consensus */ Color c = viewport - .getViewportColourScheme().findColour('A', 0, seq); + .getResidueShading().findColour('A', 0, seq); assertEquals(c, over40); /* @@ -98,7 +98,7 @@ public class PIDColourSchemeTest */ viewport.setIgnoreGapsConsensus(true, af.alignPanel); c = viewport - .getViewportColourScheme().findColour('A', 0, seq); + .getResidueShading().findColour('A', 0, seq); assertEquals(c, over60); } } -- 1.7.10.2