X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationColourChooser.java;h=f2036de5f178ed58ee773f7bc4f745f57713fc6b;hb=72c628be04c81e9a9748edc65e710045d6410980;hp=46891f8c45f385094ca1808da3f0efc56a3ee756;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java index 46891f8..f2036de 100755 --- a/src/jalview/gui/AnnotationColourChooser.java +++ b/src/jalview/gui/AnnotationColourChooser.java @@ -1,13 +1,13 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) - * Copyright (C) 2010 J Procter, AM Waterhouse, 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 @@ -21,9 +21,13 @@ import java.util.*; import java.awt.*; import java.awt.event.*; + import javax.swing.*; import javax.swing.event.*; +import net.miginfocom.swing.MigLayout; + +import jalview.bin.Cache; import jalview.datamodel.*; import jalview.schemes.*; import java.awt.Dimension; @@ -43,18 +47,19 @@ 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) { oldcs = av.getGlobalColourScheme(); - if (av.alignment.getGroups() != null) + if (av.getAlignment().getGroups() != null) { oldgroupColours = new Hashtable(); - Vector allGroups = ap.av.alignment.getGroups(); - SequenceGroup sg; - for (int g = 0; g < allGroups.size(); g++) + for (SequenceGroup sg : ap.av.getAlignment().getGroups()) { - sg = (SequenceGroup) allGroups.get(g); if (sg.cs != null) { oldgroupColours.put(sg, sg.cs); @@ -66,7 +71,7 @@ public class AnnotationColourChooser extends JPanel frame = new JInternalFrame(); frame.setContentPane(this); frame.setLayer(JLayeredPane.PALETTE_LAYER); - Desktop.addInternalFrame(frame, "Colour by Annotation", 480, 145); + Desktop.addInternalFrame(frame, "Colour by Annotation", 520, 215); slider.addChangeListener(new ChangeListener() { @@ -75,53 +80,86 @@ 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); } }); - if (av.alignment.getAlignmentAnnotation() == null) + if (av.getAlignment().getAlignmentAnnotation() == null) { return; } + // Always get default shading from preferences. + setDefaultMinMax(); + if (oldcs instanceof AnnotationColourGradient) { AnnotationColourGradient acg = (AnnotationColourGradient) oldcs; - minColour.setBackground(acg.getMinColour()); - maxColour.setBackground(acg.getMaxColour()); - } - else - { - minColour.setBackground(Color.orange); - maxColour.setBackground(Color.red); + currentColours.setSelected(acg.predefinedColours); + if (!acg.predefinedColours) + { + 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.alignment.getAlignmentAnnotation().length; i++) - { - String label = av.alignment.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"); threshold.addItem("Below Threshold"); + if (oldcs instanceof AnnotationColourGradient) + { + AnnotationColourGradient acg = (AnnotationColourGradient) oldcs; + annotations.setSelectedItem(acg.getAnnotation()); + switch (acg.getAboveThreshold()) + { + case AnnotationColourGradient.NO_THRESHOLD: + threshold.setSelectedItem("No Threshold"); + break; + case AnnotationColourGradient.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."); + } + thresholdIsMin.setSelected(acg.thresholdIsMinMax); + thresholdValue.setText("" + acg.getAnnotationThreshold()); + } + try { jbInit(); @@ -132,7 +170,57 @@ public class AnnotationColourChooser extends JPanel adjusting = false; changeColour(); + frame.invalidate(); + frame.pack(); + + } + + 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)); } public AnnotationColourChooser() @@ -148,7 +236,7 @@ public class AnnotationColourChooser extends JPanel private void jbInit() throws Exception { - minColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + minColour.setFont(JvSwingUtils.getLabelFont()); minColour.setBorder(BorderFactory.createEtchedBorder()); minColour.setPreferredSize(new Dimension(40, 20)); minColour.setToolTipText("Minimum Colour"); @@ -162,7 +250,7 @@ public class AnnotationColourChooser extends JPanel } } }); - maxColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + maxColour.setFont(JvSwingUtils.getLabelFont()); maxColour.setBorder(BorderFactory.createEtchedBorder()); maxColour.setPreferredSize(new Dimension(40, 20)); maxColour.setToolTipText("Maximum Colour"); @@ -194,8 +282,20 @@ public class AnnotationColourChooser extends JPanel cancel_actionPerformed(e); } }); - this.setLayout(borderLayout1); - jPanel2.setLayout(flowLayout1); + defColours.setOpaque(false); + defColours.setText("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) @@ -203,8 +303,6 @@ public class AnnotationColourChooser extends JPanel annotations_actionPerformed(e); } }); - jPanel1.setBackground(Color.white); - jPanel2.setBackground(Color.white); threshold.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -212,7 +310,6 @@ public class AnnotationColourChooser extends JPanel threshold_actionPerformed(e); } }); - jPanel3.setLayout(flowLayout2); thresholdValue.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -228,8 +325,7 @@ public class AnnotationColourChooser extends JPanel slider.setPreferredSize(new Dimension(100, 32)); thresholdValue.setEnabled(false); thresholdValue.setColumns(7); - jPanel3.setBackground(Color.white); - currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + currentColours.setFont(JvSwingUtils.getLabelFont()); currentColours.setOpaque(false); currentColours.setText("Use Original Colours"); currentColours.addActionListener(new ActionListener() @@ -240,6 +336,7 @@ public class AnnotationColourChooser extends JPanel } }); thresholdIsMin.setBackground(Color.white); + thresholdIsMin.setFont(JvSwingUtils.getLabelFont()); thresholdIsMin.setText("Threshold is Min/Max"); thresholdIsMin.addActionListener(new ActionListener() { @@ -248,27 +345,89 @@ public class AnnotationColourChooser extends JPanel thresholdIsMin_actionPerformed(actionEvent); } }); + seqAssociated.setBackground(Color.white); + seqAssociated.setFont(JvSwingUtils.getLabelFont()); + seqAssociated.setText("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]", "[][][]")); + 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); - jPanel2.add(minColour); - jPanel2.add(maxColour); - this.add(jPanel3, java.awt.BorderLayout.CENTER); - jPanel3.add(threshold); - jPanel3.add(slider); - jPanel3.add(thresholdValue); - jPanel3.add(thresholdIsMin); + JPanel colpanel = new JPanel(new FlowLayout()); + colpanel.setBackground(Color.white); + colpanel.add(minColour); + colpanel.add(maxColour); + jPanel2.add(colpanel, "wrap"); + jPanel2.add(threshold); + jPanel2.add(defColours, "skip 1, wrap"); + jPanel2.add(thresholdIsMin); + jPanel2.add(slider, "grow"); + jPanel2.add(thresholdValue, "grow"); this.add(jPanel1, java.awt.BorderLayout.SOUTH); - this.add(jPanel2, java.awt.BorderLayout.NORTH); + this.add(jPanel2, java.awt.BorderLayout.CENTER); + this.validate(); + } + + protected void seqAssociated_actionPerformed(ActionEvent arg0) + { + 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) + { + setDefaultMinMax(); + changeColour(); } JComboBox annotations; + int[] annmap; + JPanel minColour = new JPanel(); JPanel maxColour = new JPanel(); + JButton defColours = new JButton(); + JButton ok = new JButton(); JButton cancel = new JButton(); @@ -281,12 +440,6 @@ public class AnnotationColourChooser extends JPanel JComboBox threshold = new JComboBox(); - FlowLayout flowLayout1 = new FlowLayout(); - - JPanel jPanel3 = new JPanel(); - - FlowLayout flowLayout2 = new FlowLayout(); - JSlider slider = new JSlider(); JTextField thresholdValue = new JTextField(20); @@ -295,6 +448,8 @@ public class AnnotationColourChooser extends JPanel JCheckBox thresholdIsMin = new JCheckBox(); + JCheckBox seqAssociated = new JCheckBox(); + public void minColour_actionPerformed() { Color col = JColorChooser.showDialog(this, @@ -327,8 +482,8 @@ public class AnnotationColourChooser extends JPanel return; } - currentAnnotation = av.alignment.getAlignmentAnnotation()[annotations - .getSelectedIndex()]; + currentAnnotation = av.getAlignment().getAlignmentAnnotation()[annmap[annotations + .getSelectedIndex()]]; int aboveThreshold = -1; if (threshold.getSelectedItem().equals("Above Threshold")) @@ -342,12 +497,14 @@ public class AnnotationColourChooser extends JPanel slider.setEnabled(true); thresholdValue.setEnabled(true); + thresholdIsMin.setEnabled(true); if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD) { slider.setEnabled(false); thresholdValue.setEnabled(false); thresholdValue.setText(""); + thresholdIsMin.setEnabled(false); } else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD && currentAnnotation.threshold == null) @@ -377,14 +534,16 @@ public class AnnotationColourChooser extends JPanel AnnotationColourGradient acg = null; if (currentColours.isSelected()) { - acg = new AnnotationColourGradient(currentAnnotation, av - .getGlobalColourScheme(), aboveThreshold); + acg = new AnnotationColourGradient(currentAnnotation, + av.getGlobalColourScheme(), aboveThreshold); } else { - acg = new AnnotationColourGradient(currentAnnotation, minColour - .getBackground(), maxColour.getBackground(), aboveThreshold); + acg = new AnnotationColourGradient(currentAnnotation, + minColour.getBackground(), maxColour.getBackground(), + aboveThreshold); } + acg.setSeqAssociated(seqAssociated.isSelected()); if (currentAnnotation.graphMin == 0f && currentAnnotation.graphMax == 0f) @@ -396,14 +555,11 @@ public class AnnotationColourChooser extends JPanel av.setGlobalColourScheme(acg); - if (av.alignment.getGroups() != null) + if (av.getAlignment().getGroups() != null) { - Vector allGroups = ap.av.alignment.getGroups(); - SequenceGroup sg; - for (int g = 0; g < allGroups.size(); g++) - { - sg = (SequenceGroup) allGroups.get(g); + for (SequenceGroup sg : ap.av.getAlignment().getGroups()) + { if (sg.cs == null) { continue; @@ -413,18 +569,25 @@ public class AnnotationColourChooser extends JPanel { sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs, aboveThreshold); + ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated + .isSelected()); + } else { - sg.cs = new AnnotationColourGradient(currentAnnotation, minColour - .getBackground(), maxColour.getBackground(), + sg.cs = new AnnotationColourGradient(currentAnnotation, + minColour.getBackground(), maxColour.getBackground(), aboveThreshold); + ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated + .isSelected()); } } } - - ap.paintAlignment(false); + ap.alignmentChanged(); + // ensure all associated views (overviews, structures, etc) are notified of + // updated colours. + ap.paintAlignment(true); } public void ok_actionPerformed(ActionEvent e) @@ -441,6 +604,8 @@ public class AnnotationColourChooser extends JPanel public void cancel_actionPerformed(ActionEvent e) { reset(); + // ensure all original colouring is propagated to listeners. + ap.paintAlignment(true); try { frame.setClosed(true); @@ -452,13 +617,11 @@ public class AnnotationColourChooser extends JPanel void reset() { av.setGlobalColourScheme(oldcs); - if (av.alignment.getGroups() != null) + if (av.getAlignment().getGroups() != null) { - Vector allGroups = ap.av.alignment.getGroups(); - SequenceGroup sg; - for (int g = 0; g < allGroups.size(); g++) + + for (SequenceGroup sg : ap.av.getAlignment().getGroups()) { - sg = (SequenceGroup) allGroups.get(g); sg.cs = (ColourSchemeI) oldgroupColours.get(sg); } } @@ -490,18 +653,38 @@ 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())