X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationColourChooser.java;h=8de751a74c264438a823d3d2e29fb478316a418c;hb=3d0101179759ef157b088ea135423cd909512d9f;hp=79d2f1f986468d365b34d5987abfc887139dbc32;hpb=37de9310bec3501cbc6381e0c3dcb282fcaad812;p=jalview.git diff --git a/src/jalview/appletgui/AnnotationColourChooser.java b/src/jalview/appletgui/AnnotationColourChooser.java index 79d2f1f..8de751a 100644 --- a/src/jalview/appletgui/AnnotationColourChooser.java +++ b/src/jalview/appletgui/AnnotationColourChooser.java @@ -46,7 +46,8 @@ import java.awt.event.ItemEvent; import java.awt.event.ItemListener; import java.awt.event.MouseEvent; import java.awt.event.MouseListener; -import java.util.Hashtable; +import java.util.HashMap; +import java.util.Map; import java.util.Vector; public class AnnotationColourChooser extends Panel implements @@ -60,9 +61,15 @@ public class AnnotationColourChooser extends Panel implements ColourSchemeI oldcs; - Hashtable oldgroupColours; + Map oldgroupColours; - jalview.datamodel.AlignmentAnnotation currentAnnotation; + /* + * map from annotation to its menu item display label + * - so we know which item to pre-select on restore + */ + private Map annotationLabels; + + AlignmentAnnotation currentAnnotation; boolean adjusting = false; @@ -78,17 +85,10 @@ public class AnnotationColourChooser extends Panel implements oldcs = av.getGlobalColourScheme(); if (av.getAlignment().getGroups() != null) { - oldgroupColours = new Hashtable(); + oldgroupColours = new HashMap(); for (SequenceGroup sg : ap.av.getAlignment().getGroups()) { - if (sg.cs != null) - { - oldgroupColours.put(sg, sg.cs); - } - else - { - oldgroupColours.put(sg, "null"); - } + oldgroupColours.put(sg, sg.getColourScheme()); } } this.av = av; @@ -109,8 +109,8 @@ public class AnnotationColourChooser extends Panel implements if (oldcs instanceof AnnotationColourGradient) { AnnotationColourGradient acg = (AnnotationColourGradient) oldcs; - currentColours.setState(acg.isPredefinedColours() - || acg.getBaseColour() != null); + currentColours.setState( + acg.isPredefinedColours() || acg.getBaseColour() != null); if (!acg.isPredefinedColours() && acg.getBaseColour() == null) { minColour.setBackground(acg.getMinColour()); @@ -119,24 +119,7 @@ public class AnnotationColourChooser extends Panel implements // seqAssociated.setState(acg.isSeqAssociated()); } - Vector list = new Vector(); - int index = 1; - for (int i = 0; i < anns.length; i++) - { - String label = anns[i].label; - if (anns[i].sequenceRef != null) - { - label = label + "_" + anns[i].sequenceRef.getName(); - } - if (!list.contains(label)) - { - list.addElement(label); - } - else - { - list.addElement(label + "_" + (index++)); - } - } + Vector list = getAnnotationItems(); for (int i = 0; i < list.size(); i++) { @@ -153,7 +136,8 @@ public class AnnotationColourChooser extends Panel implements if (oldcs instanceof AnnotationColourGradient) { AnnotationColourGradient acg = (AnnotationColourGradient) oldcs; - annotations.select(acg.getAnnotation()); + String label = annotationLabels.get(acg.getAnnotation()); + annotations.select(label); switch (acg.getAboveThreshold()) { case AnnotationColourGradient.NO_THRESHOLD: @@ -166,11 +150,10 @@ public class AnnotationColourChooser extends Panel implements threshold.select(1); break; default: - throw new Error( - MessageManager - .getString("error.implementation_error_dont_know_threshold_annotationcolourgradient")); + throw new Error(MessageManager.getString( + "error.implementation_error_dont_know_threshold_annotationcolourgradient")); } - thresholdIsMin.setState(acg.thresholdIsMinMax); + thresholdIsMin.setState(acg.isThresholdIsMinMax()); thresholdValue.setText("" + acg.getAnnotationThreshold()); } @@ -186,12 +169,57 @@ public class AnnotationColourChooser extends Panel implements validate(); } + /** + * Builds and returns a list of menu items (display text) for choice of + * annotation. Also builds a map between annotations and their display labels. + * + * @return + */ + protected Vector getAnnotationItems() + { + // TODO remove duplication with gui.AnnotationRowFilter + // TODO add 'per sequence only' option / parameter + + annotationLabels = new HashMap(); + Vector list = new Vector(); + AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation(); + if (anns == null) + { + return list; + } + int index = 1; + for (int i = 0; i < anns.length; i++) + { + String label = anns[i].label; + if (anns[i].sequenceRef != null) + { + /* + * be helpful and include sequence id in label for + * sequence-associated annotation (JAL-2236) + */ + label = label + "_" + anns[i].sequenceRef.getName(); + } + if (!list.contains(label)) + { + list.addElement(label); + annotationLabels.put(anns[i], label); + } + else + { + label = label + "_" + (index++); + list.addElement(label); + annotationLabels.put(anns[i], label); + } + } + return list; + } + private void setDefaultMinMax() { minColour.setBackground(av.applet.getDefaultColourParameter( "ANNOTATIONCOLOUR_MIN", Color.orange)); - maxColour.setBackground(av.applet.getDefaultColourParameter( - "ANNOTATIONCOLOUR_MAX", Color.red)); + maxColour.setBackground(av.applet + .getDefaultColourParameter("ANNOTATIONCOLOUR_MAX", Color.red)); } @@ -236,13 +264,13 @@ public class AnnotationColourChooser extends Panel implements thresholdValue.setEnabled(false); thresholdValue.setColumns(5); currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - currentColours.setLabel(MessageManager - .getString("label.use_original_colours")); + currentColours.setLabel( + MessageManager.getString("label.use_original_colours")); currentColours.addItemListener(this); thresholdIsMin.setBackground(Color.white); - thresholdIsMin.setLabel(MessageManager - .getString("label.threshold_minmax")); + thresholdIsMin + .setLabel(MessageManager.getString("label.threshold_minmax")); this.setLayout(borderLayout1); @@ -382,8 +410,8 @@ public class AnnotationColourChooser extends Panel implements if (!adjusting) { thresholdValue.setText((slider.getValue() / 1000f) + ""); - if (currentColours.getState() - && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient)) + if (currentColours.getState() && !(av + .getGlobalColourScheme() instanceof AnnotationColourGradient)) { changeColour(); } @@ -438,8 +466,8 @@ public class AnnotationColourChooser extends Panel implements return; } - currentAnnotation = av.getAlignment().getAlignmentAnnotation()[annotations - .getSelectedIndex()]; + currentAnnotation = av.getAlignment() + .getAlignmentAnnotation()[annotations.getSelectedIndex()]; int aboveThreshold = -1; if (threshold.getSelectedIndex() == 1) @@ -465,10 +493,10 @@ public class AnnotationColourChooser extends Panel implements else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD && currentAnnotation.threshold == null) { - currentAnnotation - .setThreshold(new jalview.datamodel.GraphLine( - (currentAnnotation.graphMax - currentAnnotation.graphMin) / 2f, - "Threshold", Color.black)); + currentAnnotation.setThreshold(new jalview.datamodel.GraphLine( + (currentAnnotation.graphMax - currentAnnotation.graphMin) + / 2f, + "Threshold", Color.black)); } if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD) @@ -487,8 +515,6 @@ public class AnnotationColourChooser extends Panel implements AnnotationColourGradient acg = null; if (currentColours.getState()) { - acg = new AnnotationColourGradient(currentAnnotation, - av.getGlobalColourScheme(), aboveThreshold); } else { @@ -503,7 +529,7 @@ public class AnnotationColourChooser extends Panel implements acg.setPredefinedColours(true); } - acg.thresholdIsMinMax = thresholdIsMin.getState(); + acg.setThresholdIsMinMax(thresholdIsMin.getState()); av.setGlobalColourScheme(acg); @@ -512,24 +538,22 @@ 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, + sg.setColourScheme(new AnnotationColourGradient(currentAnnotation, minColour.getBackground(), maxColour.getBackground(), - aboveThreshold); + aboveThreshold)); } - } } @@ -545,20 +569,10 @@ public class AnnotationColourChooser extends Panel implements { for (SequenceGroup sg : ap.av.getAlignment().getGroups()) { - Object cs = oldgroupColours.get(sg); - if (cs instanceof ColourSchemeI) - { - sg.cs = (ColourSchemeI) cs; - } - else - { - // probably the "null" string we set it to if it was null originally. - sg.cs = null; - } + sg.setColourScheme(oldgroupColours.get(sg)); } } ap.paintAlignment(true); - } @Override