X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationColourChooser.java;h=965770ce5a7bbc4f7a57821d2f365b94ca089951;hb=9d465da4f21e403c20b835264929906b538c0c9b;hp=e5820723478634d8812f1efa10ca0b87f93ad327;hpb=d8fcaf315395d614059f4345c20ff2f86a4476f1;p=jalview.git diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java index e582072..965770c 100644 --- a/src/jalview/gui/AnnotationColourChooser.java +++ b/src/jalview/gui/AnnotationColourChooser.java @@ -48,7 +48,6 @@ import jalview.gui.JalviewColourChooser.ColourChooserListener; import jalview.schemes.AnnotationColourGradient; import jalview.schemes.ColourSchemeI; import jalview.util.MessageManager; -import net.bytebuddy.dynamic.DynamicType.Builder.MethodDefinition.ParameterDefinition.Initial; import net.miginfocom.swing.MigLayout; @SuppressWarnings("serial") @@ -74,9 +73,11 @@ public class AnnotationColourChooser extends AnnotationRowFilter public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap) { - this(av,ap,null); + this(av, ap, null); } - public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap,AnnotationColourGradient initSettings) + + public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap, + AnnotationColourGradient initSettings) { super(av, ap); oldcs = av.getGlobalColourScheme(); @@ -111,15 +112,17 @@ public class AnnotationColourChooser extends AnnotationRowFilter setDefaultMinMax(); adjusting = true; - if (oldcs instanceof AnnotationColourGradient && initSettings==null) + if (oldcs instanceof AnnotationColourGradient && initSettings == null) { // init from oldcs initialiseFrom((AnnotationColourGradient) oldcs); - } else { + } + else + { // use initial colour gradient - if any.. initialiseFrom(initSettings); } - + jbInit(); adjusting = false; @@ -127,12 +130,13 @@ public class AnnotationColourChooser extends AnnotationRowFilter frame.invalidate(); frame.pack(); } + private void initialiseFrom(AnnotationColourGradient acg) { - if (acg!=null) + if (acg != null) { useOriginalColours.setSelected( - acg.isPredefinedColours() || acg.getBaseColour() != null); + acg.isPredefinedColours() || acg.getBaseColour() != null); if (!acg.isPredefinedColours() && acg.getBaseColour() == null) { minColour.setBackground(acg.getMinColour()); @@ -147,10 +151,11 @@ public class AnnotationColourChooser extends AnnotationRowFilter populateThresholdComboBox(threshold); - if (acg!=null) + if (acg != null) { String label = getAnnotationMenuLabel(acg.getAnnotation()); - // TODO: workaround below shouldn't be necessary - there's a bug in getAnnotationMenuLabel! + // TODO: workaround below shouldn't be necessary - there's a bug in + // getAnnotationMenuLabel! if (acg.isSeqAssociated()) { label = acg.getAnnotation().label; @@ -376,8 +381,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter return; } - int selIndex = annotations - .getSelectedIndex(); + int selIndex = annotations.getSelectedIndex(); int annIndex = annmap[selIndex]; setCurrentAnnotation( av.getAlignment().getAlignmentAnnotation()[annIndex]); @@ -476,26 +480,34 @@ public class AnnotationColourChooser extends AnnotationRowFilter * @param av * @param ap * @param alignmentAnnotation - * @param perseq - when true, enable per-sequence if alignment annotation is per sequence + * @param perseq + * - when true, enable per-sequence if alignment annotation is per + * sequence */ public static void displayFor(AlignViewport av, AlignmentPanel ap, AlignmentAnnotation alignmentAnnotation, boolean perSeq) { ColourSchemeI global = av.getGlobalColourScheme(); - AnnotationColourGradient newCS = new AnnotationColourGradient(alignmentAnnotation, global, alignmentAnnotation.threshold!=null ? AnnotationColourGradient.ABOVE_THRESHOLD:AnnotationColourGradient.NO_THRESHOLD); - if (alignmentAnnotation.sequenceRef!=null) + AnnotationColourGradient newCS = new AnnotationColourGradient( + alignmentAnnotation, global, + alignmentAnnotation.threshold != null + ? AnnotationColourGradient.ABOVE_THRESHOLD + : AnnotationColourGradient.NO_THRESHOLD); + if (alignmentAnnotation.sequenceRef != null) { newCS.setSeqAssociated(perSeq); } - for (int i=0;i