X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationColourChooser.java;h=487b75ccc3cd25709d5913f1a943726d89f8df47;hb=0935f3c68446aa5cd3a928295a0c5ea78f303648;hp=cc2e5304127415899712455644c4eec66e39be1e;hpb=1d4b37e9bd54c095aa00e643b741c931eb61c58b;p=jalview.git diff --git a/src/jalview/appletgui/AnnotationColourChooser.java b/src/jalview/appletgui/AnnotationColourChooser.java index cc2e530..487b75c 100644 --- a/src/jalview/appletgui/AnnotationColourChooser.java +++ b/src/jalview/appletgui/AnnotationColourChooser.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 ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,6 +20,7 @@ */ package jalview.appletgui; +import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.SequenceGroup; import jalview.schemes.AnnotationColourGradient; import jalview.schemes.ColourSchemeI; @@ -80,9 +81,9 @@ public class AnnotationColourChooser extends Panel implements oldgroupColours = new Hashtable(); for (SequenceGroup sg : ap.av.getAlignment().getGroups()) { - if (sg.cs != null) + if (sg.getColourScheme() != null) { - oldgroupColours.put(sg, sg.cs); + oldgroupColours.put(sg, sg.getColourScheme()); } else { @@ -96,7 +97,8 @@ public class AnnotationColourChooser extends Panel implements slider.addAdjustmentListener(this); slider.addMouseListener(this); - if (av.getAlignment().getAlignmentAnnotation() == null) + AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation(); + if (anns == null) { return; } @@ -117,11 +119,15 @@ public class AnnotationColourChooser extends Panel implements // seqAssociated.setState(acg.isSeqAssociated()); } - Vector list = new Vector(); + Vector list = new Vector(); int index = 1; - for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++) + for (int i = 0; i < anns.length; i++) { - String label = av.getAlignment().getAlignmentAnnotation()[i].label; + String label = anns[i].label; + if (anns[i].sequenceRef != null) + { + label = label + "_" + anns[i].sequenceRef.getName(); + } if (!list.contains(label)) { list.addElement(label); @@ -138,11 +144,11 @@ public class AnnotationColourChooser extends Panel implements } threshold.addItem(MessageManager - .getString("label.threshold_feature_no_thereshold")); + .getString("label.threshold_feature_no_threshold")); threshold.addItem(MessageManager - .getString("label.threshold_feature_above_thereshold")); + .getString("label.threshold_feature_above_threshold")); threshold.addItem(MessageManager - .getString("label.threshold_feature_below_thereshold")); + .getString("label.threshold_feature_below_threshold")); if (oldcs instanceof AnnotationColourGradient) { @@ -162,7 +168,7 @@ public class AnnotationColourChooser extends Panel implements default: throw new Error( MessageManager - .getString("error.implementation_error_dont_know_thereshold_annotationcolourgradient")); + .getString("error.implementation_error_dont_know_threshold_annotationcolourgradient")); } thresholdIsMin.setState(acg.thresholdIsMinMax); thresholdValue.setText("" + acg.getAnnotationThreshold()); @@ -309,6 +315,7 @@ public class AnnotationColourChooser extends Panel implements Checkbox thresholdIsMin = new Checkbox(); + @Override public void actionPerformed(ActionEvent evt) { if (evt.getSource() == thresholdValue) @@ -336,7 +343,6 @@ public class AnnotationColourChooser extends Panel implements } else if (evt.getSource() == ok) { - changeColour(); frame.setVisible(false); } else if (evt.getSource() == cancel) @@ -352,6 +358,7 @@ public class AnnotationColourChooser extends Panel implements } } + @Override public void itemStateChanged(ItemEvent evt) { if (evt.getSource() == currentColours) @@ -369,6 +376,7 @@ public class AnnotationColourChooser extends Panel implements changeColour(); } + @Override public void adjustmentValueChanged(AdjustmentEvent evt) { if (!adjusting) @@ -479,8 +487,6 @@ public class AnnotationColourChooser extends Panel implements AnnotationColourGradient acg = null; if (currentColours.getState()) { - acg = new AnnotationColourGradient(currentAnnotation, - av.getGlobalColourScheme(), aboveThreshold); } else { @@ -505,21 +511,21 @@ public class AnnotationColourChooser extends Panel implements for (SequenceGroup sg : ap.av.getAlignment().getGroups()) { - if (sg.cs == null) + if (sg.getColourScheme() == null) { continue; } if (currentColours.getState()) { - sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs, - aboveThreshold); + sg.setColourScheme(new AnnotationColourGradient( + currentAnnotation, sg.getColourScheme(), aboveThreshold)); } else { - sg.cs = new AnnotationColourGradient(currentAnnotation, - minColour.getBackground(), maxColour.getBackground(), - aboveThreshold); + sg.setColourScheme(new AnnotationColourGradient( + currentAnnotation, minColour.getBackground(), maxColour + .getBackground(), aboveThreshold)); } } @@ -540,12 +546,12 @@ public class AnnotationColourChooser extends Panel implements Object cs = oldgroupColours.get(sg); if (cs instanceof ColourSchemeI) { - sg.cs = (ColourSchemeI) cs; + sg.setColourScheme((ColourSchemeI) cs); } else { // probably the "null" string we set it to if it was null originally. - sg.cs = null; + sg.setColourScheme(null); } } } @@ -553,23 +559,28 @@ public class AnnotationColourChooser extends Panel implements } + @Override public void mouseClicked(MouseEvent evt) { } + @Override public void mousePressed(MouseEvent evt) { } + @Override public void mouseReleased(MouseEvent evt) { ap.paintAlignment(true); } + @Override public void mouseEntered(MouseEvent evt) { } + @Override public void mouseExited(MouseEvent evt) { }