X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationColourChooser.java;h=5ee69f2d21f84a83f863f01c5c5c9b63baf2d75b;hb=6fb502e4a8749d1d98f5442c3b8156ab47996b77;hp=5b695342c0017acf7b33e9ac99d6474071e042ff;hpb=07920f27faf9a94b968d97382c59398dbb7290d8;p=jalview.git diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java old mode 100755 new mode 100644 index 5b69534..5ee69f2 --- a/src/jalview/gui/AnnotationColourChooser.java +++ b/src/jalview/gui/AnnotationColourChooser.java @@ -1,13 +1,13 @@ /* - * 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) + * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle * * 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 @@ -30,6 +30,8 @@ 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 +49,10 @@ 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) { @@ -54,7 +60,7 @@ public class AnnotationColourChooser extends JPanel if (av.getAlignment().getGroups() != null) { oldgroupColours = new Hashtable(); - for (SequenceGroup sg:ap.av.getAlignment().getGroups()) + for (SequenceGroup sg : ap.av.getAlignment().getGroups()) { if (sg.cs != null) { @@ -76,14 +82,32 @@ 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); } }); @@ -95,31 +119,22 @@ 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()); + minColour.setBackground(acg.getMinColour()); maxColour.setBackground(acg.getMaxColour()); } seqAssociated.setSelected(acg.isSeqAssociated()); + } - adjusting = true; - 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++)); - } - - annotations = new JComboBox(list); + annotations = new JComboBox( + getAnnotationItems(seqAssociated.isSelected())); threshold.addItem("No Threshold"); threshold.addItem("Above Threshold"); @@ -129,21 +144,23 @@ public class AnnotationColourChooser extends JPanel { AnnotationColourGradient acg = (AnnotationColourGradient) oldcs; annotations.setSelectedItem(acg.getAnnotation()); - switch (acg.getAboveThreshold()) { + switch (acg.getAboveThreshold()) + { case AnnotationColourGradient.NO_THRESHOLD: - threshold.setSelectedItem("No Threshold"); + threshold.setSelectedItem("No Threshold"); break; case AnnotationColourGradient.ABOVE_THRESHOLD: - threshold.setSelectedItem("Above Threshold"); + threshold.setSelectedItem("Above Threshold"); break; case AnnotationColourGradient.BELOW_THRESHOLD: threshold.setSelectedItem("Below Threshold"); break; - default: - throw new Error("Implementation error: don't know about threshold setting for current AnnotationColourGradient."); + default: + throw new Error( + "Implementation error: don't know about threshold setting for current AnnotationColourGradient."); } thresholdIsMin.setSelected(acg.thresholdIsMinMax); - thresholdValue.setText(""+acg.getAnnotationThreshold()); + thresholdValue.setText("" + acg.getAnnotationThreshold()); } try @@ -161,10 +178,52 @@ public class AnnotationColourChooser extends JPanel } + private Vector getAnnotationItems(boolean isSeqAssociated) + { + Vector list = new Vector(); + int index = 1; + int[] anmap = new int[av.getAlignment().getAlignmentAnnotation().length]; + boolean enableSeqAss = false; + for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++) + { + if (av.getAlignment().getAlignmentAnnotation()[i].sequenceRef == null) + { + if (isSeqAssociated) + { + continue; + } + } + else + { + enableSeqAss = true; + } + String label = av.getAlignment().getAlignmentAnnotation()[i].label; + if (!list.contains(label)) + { + anmap[list.size()] = i; + list.addElement(label); + + } + else + { + if (!isSeqAssociated) + { + anmap[list.size()] = i; + list.addElement(label + "_" + (index++)); + } + } + } + seqAssociated.setEnabled(enableSeqAss); + annmap = new int[list.size()]; + System.arraycopy(anmap, 0, annmap, 0, annmap.length); + return list; + } private void setDefaultMinMax() { - minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange)); - maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red)); + minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", + Color.orange)); + maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", + Color.red)); } public AnnotationColourChooser() @@ -209,7 +268,7 @@ 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) @@ -218,7 +277,7 @@ 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) @@ -227,18 +286,19 @@ public class AnnotationColourChooser extends JPanel } }); defColours.setOpaque(false); - defColours.setText("Defaults"); - defColours.setToolTipText("Reset min and max colours to defaults from user preferences."); + defColours.setText(MessageManager.getString("action.set_defaults")); + defColours + .setToolTipText("Reset min and max colours to defaults from user preferences."); defColours.addActionListener(new ActionListener() { - + @Override public void actionPerformed(ActionEvent arg0) { resetColours_actionPerformed(arg0); } }); - + annotations.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -270,7 +330,7 @@ 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) @@ -280,7 +340,7 @@ 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) @@ -290,34 +350,34 @@ 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() { - + @Override public void actionPerformed(ActionEvent arg0) { seqAssociated_actionPerformed(arg0); } }); - + this.setLayout(borderLayout1); - jPanel2.setLayout(new MigLayout("","[left][center][right]","[][][]")); + jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]")); jPanel1.setBackground(Color.white); jPanel2.setBackground(Color.white); jPanel1.add(ok); jPanel1.add(cancel); - jPanel2.add(annotations); + jPanel2.add(annotations, "grow, wrap"); + jPanel2.add(seqAssociated); jPanel2.add(currentColours); JPanel colpanel = new JPanel(new FlowLayout()); colpanel.setBackground(Color.white); colpanel.add(minColour); colpanel.add(maxColour); jPanel2.add(colpanel, "wrap"); - jPanel2.add(seqAssociated, "wrap"); jPanel2.add(threshold); - jPanel2.add(defColours,"skip 1, wrap"); + jPanel2.add(defColours, "skip 1, wrap"); jPanel2.add(thresholdIsMin); jPanel2.add(slider, "grow"); jPanel2.add(thresholdValue, "grow"); @@ -328,7 +388,31 @@ public class AnnotationColourChooser extends JPanel protected void seqAssociated_actionPerformed(ActionEvent arg0) { - changeColour(); + adjusting = true; + String cursel = (String) annotations.getSelectedItem(); + boolean isvalid = false, isseqs = seqAssociated.isSelected(); + this.annotations.removeAllItems(); + for (String anitem : getAnnotationItems(seqAssociated.isSelected())) + { + if (anitem.equals(cursel) || (isseqs && cursel.startsWith(anitem))) + { + isvalid = true; + cursel = anitem; + } + this.annotations.addItem(anitem); + } + adjusting = false; + if (isvalid) + { + this.annotations.setSelectedItem(cursel); + } + else + { + if (annotations.getItemCount() > 0) + { + annotations.setSelectedIndex(0); + } + } } protected void resetColours_actionPerformed(ActionEvent arg0) @@ -339,22 +423,26 @@ public class AnnotationColourChooser extends JPanel JComboBox annotations; + int[] annmap; + JPanel minColour = new JPanel(); JPanel maxColour = new JPanel(); + JButton defColours = new JButton(); + JButton ok = new JButton(); JButton cancel = new JButton(); JPanel jPanel1 = new JPanel(); + JPanel jPanel2 = new JPanel(); - + BorderLayout borderLayout1 = new BorderLayout(); JComboBox threshold = new JComboBox(); - JSlider slider = new JSlider(); JTextField thresholdValue = new JTextField(20); @@ -362,7 +450,7 @@ public class AnnotationColourChooser extends JPanel JCheckBox currentColours = new JCheckBox(); JCheckBox thresholdIsMin = new JCheckBox(); - + JCheckBox seqAssociated = new JCheckBox(); public void minColour_actionPerformed() @@ -397,8 +485,8 @@ public class AnnotationColourChooser extends JPanel return; } - currentAnnotation = av.getAlignment().getAlignmentAnnotation()[annotations - .getSelectedIndex()]; + currentAnnotation = av.getAlignment().getAlignmentAnnotation()[annmap[annotations + .getSelectedIndex()]]; int aboveThreshold = -1; if (threshold.getSelectedItem().equals("Above Threshold")) @@ -463,7 +551,7 @@ public class AnnotationColourChooser extends JPanel if (currentAnnotation.graphMin == 0f && currentAnnotation.graphMax == 0f) { - acg.predefinedColours = true; + acg.setPredefinedColours(true); } acg.thresholdIsMinMax = thresholdIsMin.isSelected(); @@ -472,8 +560,8 @@ public class AnnotationColourChooser extends JPanel if (av.getAlignment().getGroups() != null) { - - for (SequenceGroup sg:ap.av.getAlignment().getGroups()) + + for (SequenceGroup sg : ap.av.getAlignment().getGroups()) { if (sg.cs == null) { @@ -484,7 +572,8 @@ public class AnnotationColourChooser extends JPanel { sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs, aboveThreshold); - ((AnnotationColourGradient)sg.cs).setSeqAssociated(seqAssociated.isSelected()); + ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated + .isSelected()); } else @@ -492,13 +581,15 @@ public class AnnotationColourChooser extends JPanel sg.cs = new AnnotationColourGradient(currentAnnotation, minColour.getBackground(), maxColour.getBackground(), aboveThreshold); - ((AnnotationColourGradient)sg.cs).setSeqAssociated(seqAssociated.isSelected()); + ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated + .isSelected()); } } } ap.alignmentChanged(); - // ensure all associated views (overviews, structures, etc) are notified of updated colours. + // ensure all associated views (overviews, structures, etc) are notified of + // updated colours. ap.paintAlignment(true); } @@ -516,7 +607,7 @@ public class AnnotationColourChooser extends JPanel public void cancel_actionPerformed(ActionEvent e) { reset(); - // ensure all original colouring is propagated to listeners. + // ensure all original colouring is propagated to listeners. ap.paintAlignment(true); try { @@ -531,8 +622,8 @@ public class AnnotationColourChooser extends JPanel av.setGlobalColourScheme(oldcs); if (av.getAlignment().getGroups() != null) { - - for (SequenceGroup sg:ap.av.getAlignment().getGroups()) + + for (SequenceGroup sg : ap.av.getAlignment().getGroups()) { sg.cs = (ColourSchemeI) oldgroupColours.get(sg); } @@ -565,18 +656,38 @@ 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())