X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationColourChooser.java;h=9afe54fdc0531ce963bb2757a5ec12069f440bdc;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=5a942f1e752b8b835723bdfec10b5626e5a8437c;hpb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;p=jalview.git diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java old mode 100755 new mode 100644 index 5a942f1..9afe54f --- a/src/jalview/gui/AnnotationColourChooser.java +++ b/src/jalview/gui/AnnotationColourChooser.java @@ -1,19 +1,20 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) - * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) + * Copyright (C) 2014 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. - * + * * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; @@ -30,6 +31,8 @@ import net.miginfocom.swing.MigLayout; import jalview.bin.Cache; import jalview.datamodel.*; import jalview.schemes.*; +import jalview.util.MessageManager; + import java.awt.Dimension; public class AnnotationColourChooser extends JPanel @@ -47,6 +50,10 @@ public class AnnotationColourChooser extends JPanel jalview.datamodel.AlignmentAnnotation currentAnnotation; boolean adjusting = false; + /** + * enabled if the user is dragging the slider - try to keep updates to a minimun + */ + boolean sliderDragging = false; public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap) { @@ -67,7 +74,7 @@ public class AnnotationColourChooser extends JPanel frame = new JInternalFrame(); frame.setContentPane(this); frame.setLayer(JLayeredPane.PALETTE_LAYER); - Desktop.addInternalFrame(frame, "Colour by Annotation", 520, 215); + Desktop.addInternalFrame(frame, MessageManager.getString("label.colour_by_annotation"), 520, 215); slider.addChangeListener(new ChangeListener() { @@ -76,14 +83,32 @@ public class AnnotationColourChooser extends JPanel if (!adjusting) { thresholdValue.setText(((float) slider.getValue() / 1000f) + ""); - valueChanged(); + valueChanged(!sliderDragging); } } }); slider.addMouseListener(new MouseAdapter() { + @Override + public void mousePressed(MouseEvent e) + { + sliderDragging=true; + super.mousePressed(e); + } + + @Override + public void mouseDragged(MouseEvent e) + { + sliderDragging=true; + super.mouseDragged(e); + } public void mouseReleased(MouseEvent evt) { + if (sliderDragging) + { + sliderDragging=false; + valueChanged(true); + } ap.paintAlignment(true); } }); @@ -96,24 +121,25 @@ public class AnnotationColourChooser extends JPanel // Always get default shading from preferences. setDefaultMinMax(); + adjusting = true; if (oldcs instanceof AnnotationColourGradient) { AnnotationColourGradient acg = (AnnotationColourGradient) oldcs; - currentColours.setSelected(acg.predefinedColours); - if (!acg.predefinedColours) + currentColours.setSelected(acg.isPredefinedColours() || acg.getBaseColour()!=null); + if (!acg.isPredefinedColours() && acg.getBaseColour()==null) { minColour.setBackground(acg.getMinColour()); maxColour.setBackground(acg.getMaxColour()); } seqAssociated.setSelected(acg.isSeqAssociated()); + } - adjusting = true; annotations = new JComboBox( getAnnotationItems(seqAssociated.isSelected())); - threshold.addItem("No Threshold"); - threshold.addItem("Above Threshold"); - threshold.addItem("Below Threshold"); + 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")); if (oldcs instanceof AnnotationColourGradient) { @@ -122,13 +148,13 @@ public class AnnotationColourChooser extends JPanel switch (acg.getAboveThreshold()) { case AnnotationColourGradient.NO_THRESHOLD: - threshold.setSelectedItem("No Threshold"); + threshold.setSelectedIndex(0); break; case AnnotationColourGradient.ABOVE_THRESHOLD: - threshold.setSelectedItem("Above Threshold"); + threshold.setSelectedIndex(1); break; case AnnotationColourGradient.BELOW_THRESHOLD: - threshold.setSelectedItem("Below Threshold"); + threshold.setSelectedIndex(2); break; default: throw new Error( @@ -193,7 +219,6 @@ public class AnnotationColourChooser extends JPanel System.arraycopy(anmap, 0, annmap, 0, annmap.length); return list; } - private void setDefaultMinMax() { minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", @@ -218,7 +243,7 @@ public class AnnotationColourChooser extends JPanel minColour.setFont(JvSwingUtils.getLabelFont()); minColour.setBorder(BorderFactory.createEtchedBorder()); minColour.setPreferredSize(new Dimension(40, 20)); - minColour.setToolTipText("Minimum Colour"); + minColour.setToolTipText(MessageManager.getString("label.min_colour")); minColour.addMouseListener(new MouseAdapter() { public void mousePressed(MouseEvent e) @@ -232,7 +257,7 @@ public class AnnotationColourChooser extends JPanel maxColour.setFont(JvSwingUtils.getLabelFont()); maxColour.setBorder(BorderFactory.createEtchedBorder()); maxColour.setPreferredSize(new Dimension(40, 20)); - maxColour.setToolTipText("Maximum Colour"); + maxColour.setToolTipText(MessageManager.getString("label.max_colour")); maxColour.addMouseListener(new MouseAdapter() { public void mousePressed(MouseEvent e) @@ -244,7 +269,7 @@ public class AnnotationColourChooser extends JPanel } }); ok.setOpaque(false); - ok.setText("OK"); + ok.setText(MessageManager.getString("action.ok")); ok.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -253,7 +278,7 @@ public class AnnotationColourChooser extends JPanel } }); cancel.setOpaque(false); - cancel.setText("Cancel"); + cancel.setText(MessageManager.getString("action.cancel")); cancel.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -262,9 +287,9 @@ public class AnnotationColourChooser extends JPanel } }); defColours.setOpaque(false); - defColours.setText("Defaults"); + defColours.setText(MessageManager.getString("action.set_defaults")); defColours - .setToolTipText("Reset min and max colours to defaults from user preferences."); + .setToolTipText(MessageManager.getString("label.reset_min_max_colours_to_defaults")); defColours.addActionListener(new ActionListener() { @@ -306,7 +331,7 @@ public class AnnotationColourChooser extends JPanel thresholdValue.setColumns(7); currentColours.setFont(JvSwingUtils.getLabelFont()); currentColours.setOpaque(false); - currentColours.setText("Use Original Colours"); + currentColours.setText(MessageManager.getString("label.use_original_colours")); currentColours.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -316,7 +341,7 @@ public class AnnotationColourChooser extends JPanel }); thresholdIsMin.setBackground(Color.white); thresholdIsMin.setFont(JvSwingUtils.getLabelFont()); - thresholdIsMin.setText("Threshold is Min/Max"); + thresholdIsMin.setText(MessageManager.getString("label.threshold_minmax")); thresholdIsMin.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent actionEvent) @@ -326,7 +351,7 @@ public class AnnotationColourChooser extends JPanel }); seqAssociated.setBackground(Color.white); seqAssociated.setFont(JvSwingUtils.getLabelFont()); - seqAssociated.setText("Per-sequence only"); + seqAssociated.setText(MessageManager.getString("label.per_sequence_only")); seqAssociated.addActionListener(new ActionListener() { @@ -465,11 +490,11 @@ public class AnnotationColourChooser extends JPanel .getSelectedIndex()]]; int aboveThreshold = -1; - if (threshold.getSelectedItem().equals("Above Threshold")) + if (threshold.getSelectedIndex()==1) { aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD; } - else if (threshold.getSelectedItem().equals("Below Threshold")) + else if (threshold.getSelectedIndex()==2) { aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD; } @@ -527,7 +552,7 @@ public class AnnotationColourChooser extends JPanel if (currentAnnotation.graphMin == 0f && currentAnnotation.graphMax == 0f) { - acg.predefinedColours = true; + acg.setPredefinedColours(true); } acg.thresholdIsMinMax = thresholdIsMin.isSelected(); @@ -632,18 +657,38 @@ public class AnnotationColourChooser extends JPanel } } - public void valueChanged() + public void valueChanged(boolean updateAllAnnotation) { if (currentColours.isSelected() && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient)) { changeColour(); } - currentAnnotation.threshold.value = (float) slider.getValue() / 1000f; + propagateSeqAssociatedThreshold(updateAllAnnotation); ap.paintAlignment(false); } + private void propagateSeqAssociatedThreshold(boolean allAnnotation) + { + if (currentAnnotation.sequenceRef == null + || currentAnnotation.threshold == null) + { + return; + } + // TODO: JAL-1327 only update visible annotation thresholds if allAnnotation is false, since we only need to provide a quick visual indicator + + float thr = currentAnnotation.threshold.value; + for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++) + { + AlignmentAnnotation aa = av.getAlignment().getAlignmentAnnotation()[i]; + if (aa.label.equals(currentAnnotation.label)) + { + aa.threshold.value = thr; + } + } + } + public void currentColours_actionPerformed(ActionEvent e) { if (currentColours.isSelected())