X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationColourChooser.java;h=8de751a74c264438a823d3d2e29fb478316a418c;hb=3d0101179759ef157b088ea135423cd909512d9f;hp=3e7a3fd18c0819d2a5dc484bde0b8f25a5835b70;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git diff --git a/src/jalview/appletgui/AnnotationColourChooser.java b/src/jalview/appletgui/AnnotationColourChooser.java index 3e7a3fd..8de751a 100644 --- a/src/jalview/appletgui/AnnotationColourChooser.java +++ b/src/jalview/appletgui/AnnotationColourChooser.java @@ -1,32 +1,55 @@ /* - * 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. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.appletgui; -import java.util.*; - -import java.awt.*; -import java.awt.event.*; - -import jalview.datamodel.*; -import jalview.schemes.*; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.SequenceGroup; +import jalview.schemes.AnnotationColourGradient; +import jalview.schemes.ColourSchemeI; import jalview.util.MessageManager; +import java.awt.BorderLayout; +import java.awt.Button; +import java.awt.Checkbox; +import java.awt.Choice; +import java.awt.Color; +import java.awt.Dimension; +import java.awt.FlowLayout; +import java.awt.Font; +import java.awt.Frame; +import java.awt.Panel; +import java.awt.Scrollbar; +import java.awt.TextField; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.AdjustmentEvent; +import java.awt.event.AdjustmentListener; +import java.awt.event.ItemEvent; +import java.awt.event.ItemListener; +import java.awt.event.MouseEvent; +import java.awt.event.MouseListener; +import java.util.HashMap; +import java.util.Map; +import java.util.Vector; + public class AnnotationColourChooser extends Panel implements ActionListener, AdjustmentListener, ItemListener, MouseListener { @@ -38,9 +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; @@ -56,17 +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; @@ -75,7 +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; } @@ -86,8 +109,9 @@ public class AnnotationColourChooser extends Panel implements if (oldcs instanceof AnnotationColourGradient) { AnnotationColourGradient acg = (AnnotationColourGradient) oldcs; - currentColours.setState(acg.isPredefinedColours() || acg.getBaseColour()!=null); - if (!acg.isPredefinedColours() && acg.getBaseColour()==null) + currentColours.setState( + acg.isPredefinedColours() || acg.getBaseColour() != null); + if (!acg.isPredefinedColours() && acg.getBaseColour() == null) { minColour.setBackground(acg.getMinColour()); maxColour.setBackground(acg.getMaxColour()); @@ -95,31 +119,25 @@ public class AnnotationColourChooser extends Panel implements // seqAssociated.setState(acg.isSeqAssociated()); } - - Vector list = new Vector(); - int index = 1; - for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++) - { - String label = av.getAlignment().getAlignmentAnnotation()[i].label; - if (!list.contains(label)) - list.addElement(label); - else - list.addElement(label + "_" + (index++)); - } + Vector list = getAnnotationItems(); for (int i = 0; i < list.size(); i++) { annotations.addItem(list.elementAt(i).toString()); } - threshold.addItem(MessageManager.getString("label.threshold_feature_no_thereshold")); - threshold.addItem(MessageManager.getString("label.threshold_feature_above_thereshold")); - threshold.addItem(MessageManager.getString("label.threshold_feature_below_thereshold")); + threshold.addItem(MessageManager + .getString("label.threshold_feature_no_threshold")); + threshold.addItem(MessageManager + .getString("label.threshold_feature_above_threshold")); + threshold.addItem(MessageManager + .getString("label.threshold_feature_below_threshold")); 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: @@ -132,10 +150,10 @@ public class AnnotationColourChooser extends Panel implements threshold.select(1); break; default: - throw new Error( - "Implementation error: don't know about threshold setting for current 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()); } @@ -145,17 +163,63 @@ public class AnnotationColourChooser extends Panel implements frame = new Frame(); frame.add(this); - jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.colour_by_annotation"), 560, + jalview.bin.JalviewLite.addFrame(frame, + MessageManager.getString("label.colour_by_annotation"), 560, 175); 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)); } @@ -200,11 +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); @@ -277,6 +343,7 @@ public class AnnotationColourChooser extends Panel implements Checkbox thresholdIsMin = new Checkbox(); + @Override public void actionPerformed(ActionEvent evt) { if (evt.getSource() == thresholdValue) @@ -304,7 +371,6 @@ public class AnnotationColourChooser extends Panel implements } else if (evt.getSource() == ok) { - changeColour(); frame.setVisible(false); } else if (evt.getSource() == cancel) @@ -320,6 +386,7 @@ public class AnnotationColourChooser extends Panel implements } } + @Override public void itemStateChanged(ItemEvent evt) { if (evt.getSource() == currentColours) @@ -337,18 +404,19 @@ public class AnnotationColourChooser extends Panel implements changeColour(); } + @Override public void adjustmentValueChanged(AdjustmentEvent evt) { if (!adjusting) { - thresholdValue.setText(((float) slider.getValue() / 1000f) + ""); - if (currentColours.getState() - && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient)) + thresholdValue.setText((slider.getValue() / 1000f) + ""); + if (currentColours.getState() && !(av + .getGlobalColourScheme() instanceof AnnotationColourGradient)) { changeColour(); } - currentAnnotation.threshold.value = (float) slider.getValue() / 1000f; + currentAnnotation.threshold.value = slider.getValue() / 1000f; ap.paintAlignment(false); } } @@ -398,15 +466,15 @@ 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) + if (threshold.getSelectedIndex() == 1) { aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD; } - else if (threshold.getSelectedIndex()==2) + else if (threshold.getSelectedIndex() == 2) { aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD; } @@ -425,10 +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) @@ -447,8 +515,6 @@ public class AnnotationColourChooser extends Panel implements AnnotationColourGradient acg = null; if (currentColours.getState()) { - acg = new AnnotationColourGradient(currentAnnotation, - av.getGlobalColourScheme(), aboveThreshold); } else { @@ -463,7 +529,7 @@ public class AnnotationColourChooser extends Panel implements acg.setPredefinedColours(true); } - acg.thresholdIsMinMax = thresholdIsMin.getState(); + acg.setThresholdIsMinMax(thresholdIsMin.getState()); av.setGlobalColourScheme(acg); @@ -472,24 +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)); } - } } @@ -505,39 +569,34 @@ 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 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) { }