X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureColourChooser.java;h=68052d0d66cfdf12dda175072cd0ca05d64a00e9;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=55865dbc729a7fd495806bdb51eb2c8098f052b0;hpb=27926214f361deaf6bd78500fa80ac7dd4478b6b;p=jalview.git diff --git a/src/jalview/gui/FeatureColourChooser.java b/src/jalview/gui/FeatureColourChooser.java index 55865db..68052d0 100644 --- a/src/jalview/gui/FeatureColourChooser.java +++ b/src/jalview/gui/FeatureColourChooser.java @@ -1,20 +1,19 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * 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 * - * This program 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 2 - * of the License, or (at your option) any later version. + * This file is part of Jalview. * - * This program 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. + * 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. * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * 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 . */ package jalview.gui; @@ -23,44 +22,63 @@ import java.util.*; import java.awt.*; import java.awt.event.*; import javax.swing.*; +import javax.swing.border.LineBorder; import javax.swing.event.*; import jalview.datamodel.*; import jalview.schemes.*; import java.awt.Dimension; -public class FeatureColourChooser extends JPanel +public class FeatureColourChooser extends JalviewDialog { - JInternalFrame frame; - + // FeatureSettings fs; FeatureRenderer fr; - FeatureSettings fs; + private GraduatedColor cs; + + private Object oldcs; - GraduatedColor cs; - Object oldcs; + /** + * + * @return the last colour setting selected by user - either oldcs (which may + * be a java.awt.Color) or the new GraduatedColor + */ + public Object getLastColour() + { + if (cs == null) + { + return oldcs; + } + return cs; + } Hashtable oldgroupColours; - + AlignmentPanel ap; - boolean adjusting = false; private float min; private float max; + String type = null; - public FeatureColourChooser(FeatureSettings fsettings, String type) + + public FeatureColourChooser(FeatureRenderer frender, String type) + { + this(frender, false, type); + } + + public FeatureColourChooser(FeatureRenderer frender, boolean block, + String type) { - this.fs = fsettings; + this.fr = frender; this.type = type; - fr = fsettings.fr; ap = fr.ap; - frame = new JInternalFrame(); - frame.setContentPane(this); - frame.setLayer(JLayeredPane.PALETTE_LAYER); - Desktop.addInternalFrame(frame, "Graduated Feature Colour for "+type, 480, 145); + initDialogFrame(this,true, block,"Graduated Feature Colour for " + type, 480, 185); + // frame.setLayer(JLayeredPane.PALETTE_LAYER); + // Desktop.addInternalFrame(frame, "Graduated Feature Colour for "+type, + // 480, 145); slider.addChangeListener(new ChangeListener() { @@ -77,7 +95,11 @@ public class FeatureColourChooser extends JPanel { public void mouseReleased(MouseEvent evt) { - if (fr.ap!=null) { fr.ap.paintAlignment(true); }; + if (ap != null) + { + ap.paintAlignment(true); + } + ; } }); @@ -87,14 +109,18 @@ public class FeatureColourChooser extends JPanel oldcs = fr.featureColours.get(type); if (oldcs instanceof GraduatedColor) { - if (((GraduatedColor)oldcs).isAutoScale()) + if (((GraduatedColor) oldcs).isAutoScale()) { // update the scale cs = new GraduatedColor((GraduatedColor) oldcs, min, max); - } else { + } + else + { cs = new GraduatedColor((GraduatedColor) oldcs); } - } else { + } + else + { // promote original color to a graduated color Color bl = Color.black; if (oldcs instanceof Color) @@ -102,12 +128,13 @@ public class FeatureColourChooser extends JPanel bl = (Color) oldcs; } // original colour becomes the maximum colour - cs = new GraduatedColor(Color.white,bl,mm[0],mm[1]); + cs = new GraduatedColor(Color.white, bl, mm[0], mm[1]); + cs.setColourByLabel(false); } - minColour.setBackground(cs.getMinColor()); - maxColour.setBackground(cs.getMaxColor()); + minColour.setBackground(oldminColour = cs.getMinColor()); + maxColour.setBackground(oldmaxColour = cs.getMaxColor()); adjusting = true; - + try { jbInit(); @@ -116,22 +143,24 @@ public class FeatureColourChooser extends JPanel } // update the gui from threshold state thresholdIsMin.setSelected(!cs.isAutoScale()); - if (cs.getThreshType()!=AnnotationColourGradient.NO_THRESHOLD) + colourByLabel.setSelected(cs.isColourByLabel()); + if (cs.getThreshType() != AnnotationColourGradient.NO_THRESHOLD) { // initialise threshold slider and selector - threshold.setSelectedIndex(cs.getThreshType()==AnnotationColourGradient.ABOVE_THRESHOLD ? 1 : 2); - slider.setEnabled(true); + threshold + .setSelectedIndex(cs.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD ? 1 + : 2); + slider.setEnabled(true); thresholdValue.setEnabled(true); - threshline = new jalview.datamodel.GraphLine( - (max - min) / 2f, - "Threshold", Color.black); - + threshline = new jalview.datamodel.GraphLine((max - min) / 2f, + "Threshold", Color.black); + } adjusting = false; changeColour(); - + waitForInput(); } public FeatureColourChooser() @@ -147,8 +176,9 @@ public class FeatureColourChooser extends JPanel private void jbInit() throws Exception { - minColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - minColour.setBorder(BorderFactory.createEtchedBorder()); + + minColour.setFont(JvSwingUtils.getLabelFont()); + minColour.setBorder(BorderFactory.createLineBorder(Color.black)); minColour.setPreferredSize(new Dimension(40, 20)); minColour.setToolTipText("Minimum Colour"); minColour.addMouseListener(new MouseAdapter() @@ -161,8 +191,8 @@ public class FeatureColourChooser extends JPanel } } }); - maxColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - maxColour.setBorder(BorderFactory.createEtchedBorder()); + maxColour.setFont(JvSwingUtils.getLabelFont()); + maxColour.setBorder(BorderFactory.createLineBorder(Color.black)); maxColour.setPreferredSize(new Dimension(40, 20)); maxColour.setToolTipText("Maximum Colour"); maxColour.addMouseListener(new MouseAdapter() @@ -175,24 +205,11 @@ public class FeatureColourChooser extends JPanel } } }); - ok.setOpaque(false); - ok.setText("OK"); - ok.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - ok_actionPerformed(e); - } - }); - cancel.setOpaque(false); - cancel.setText("Cancel"); - cancel.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - cancel_actionPerformed(e); - } - }); + maxColour.setBorder(new LineBorder(Color.black)); + minText.setText("Min:"); + minText.setFont(JvSwingUtils.getLabelFont()); + maxText.setText("Max:"); + maxText.setFont(JvSwingUtils.getLabelFont()); this.setLayout(borderLayout1); jPanel2.setLayout(flowLayout1); jPanel1.setBackground(Color.white); @@ -204,6 +221,7 @@ public class FeatureColourChooser extends JPanel threshold_actionPerformed(e); } }); + threshold.setToolTipText("Threshold the feature display by score."); threshold.addItem("No Threshold"); // index 0 threshold.addItem("Above Threshold"); // index 1 threshold.addItem("Below Threshold"); // index 2 @@ -221,21 +239,14 @@ public class FeatureColourChooser extends JPanel slider.setEnabled(false); slider.setOpaque(false); slider.setPreferredSize(new Dimension(100, 32)); + slider.setToolTipText("Adjust threshold"); thresholdValue.setEnabled(false); thresholdValue.setColumns(7); jPanel3.setBackground(Color.white); - currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - currentColours.setOpaque(false); - currentColours.setText("Use Original Colours"); - currentColours.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - currentColours_actionPerformed(e); - } - }); thresholdIsMin.setBackground(Color.white); thresholdIsMin.setText("Threshold is Min/Max"); + thresholdIsMin + .setToolTipText("Toggle between absolute and relative display threshold."); thresholdIsMin.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent actionEvent) @@ -243,11 +254,26 @@ public class FeatureColourChooser extends JPanel thresholdIsMin_actionPerformed(actionEvent); } }); + colourByLabel.setBackground(Color.white); + colourByLabel.setText("Colour by Label"); + colourByLabel + .setToolTipText("Display features of the same type with a different label using a different colour. (e.g. domain features)"); + colourByLabel.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent actionEvent) + { + colourByLabel_actionPerformed(actionEvent); + } + }); + colourPanel.setBackground(Color.white); jPanel1.add(ok); jPanel1.add(cancel); - // jPanel2.add(currentColours); - jPanel2.add(minColour); - jPanel2.add(maxColour); + jPanel2.add(colourByLabel, java.awt.BorderLayout.WEST); + jPanel2.add(colourPanel, java.awt.BorderLayout.EAST); + colourPanel.add(minText); + colourPanel.add(minColour); + colourPanel.add(maxText); + colourPanel.add(maxColour); this.add(jPanel3, java.awt.BorderLayout.CENTER); jPanel3.add(threshold); jPanel3.add(slider); @@ -257,14 +283,15 @@ public class FeatureColourChooser extends JPanel this.add(jPanel2, java.awt.BorderLayout.NORTH); } + JLabel minText = new JLabel(); + + JLabel maxText = new JLabel(); JPanel minColour = new JPanel(); JPanel maxColour = new JPanel(); - JButton ok = new JButton(); - - JButton cancel = new JButton(); + JPanel colourPanel = new JPanel(); JPanel jPanel1 = new JPanel(); @@ -283,13 +310,20 @@ public class FeatureColourChooser extends JPanel JSlider slider = new JSlider(); JTextField thresholdValue = new JTextField(20); - // TODO refactor to tolower flag - JCheckBox currentColours = new JCheckBox(); + + // TODO implement GUI for tolower flag + // JCheckBox toLower = new JCheckBox(); JCheckBox thresholdIsMin = new JCheckBox(); + JCheckBox colourByLabel = new JCheckBox(); + private GraphLine threshline; + private Color oldmaxColour; + + private Color oldminColour; + public void minColour_actionPerformed() { Color col = JColorChooser.showDialog(this, @@ -297,6 +331,7 @@ public class FeatureColourChooser extends JPanel if (col != null) { minColour.setBackground(col); + minColour.setForeground(col); } minColour.repaint(); changeColour(); @@ -309,6 +344,7 @@ public class FeatureColourChooser extends JPanel if (col != null) { maxColour.setBackground(col); + maxColour.setForeground(col); } maxColour.repaint(); changeColour(); @@ -322,7 +358,6 @@ public class FeatureColourChooser extends JPanel return; } - int aboveThreshold = AnnotationColourGradient.NO_THRESHOLD; if (threshold.getSelectedItem().equals("Above Threshold")) { @@ -331,25 +366,36 @@ public class FeatureColourChooser extends JPanel else if (threshold.getSelectedItem().equals("Below Threshold")) { aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD; - } + } slider.setEnabled(true); thresholdValue.setEnabled(true); - GraduatedColor acg = new GraduatedColor(minColour.getBackground(), maxColour.getBackground(), min, max); + + GraduatedColor acg; + if (cs.isColourByLabel()) + { + acg = new GraduatedColor(oldminColour, oldmaxColour, min, max); + } + else + { + acg = new GraduatedColor(oldminColour = minColour.getBackground(), + oldmaxColour = maxColour.getBackground(), min, max); + + } if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD) { slider.setEnabled(false); thresholdValue.setEnabled(false); thresholdValue.setText(""); + thresholdIsMin.setEnabled(false); } else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD && threshline == null) { // todo visual indication of feature threshold - threshline = new jalview.datamodel.GraphLine( - (max - min) / 2f, - "Threshold", Color.black); + threshline = new jalview.datamodel.GraphLine((max - min) / 2f, + "Threshold", Color.black); } if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD) @@ -357,8 +403,7 @@ public class FeatureColourChooser extends JPanel adjusting = true; acg.setThresh(threshline.value); - float range = max * 1000f - - min * 1000f; + float range = max * 1000f - min * 1000f; slider.setMinimum((int) (min * 1000)); slider.setMaximum((int) (max * 1000)); @@ -367,53 +412,77 @@ public class FeatureColourChooser extends JPanel slider.setMajorTickSpacing((int) (range / 10f)); slider.setEnabled(true); thresholdValue.setEnabled(true); + thresholdIsMin.setEnabled(!colourByLabel.isSelected()); adjusting = false; } acg.setThreshType(aboveThreshold); - if (thresholdIsMin.isSelected() && aboveThreshold != AnnotationColourGradient.NO_THRESHOLD) + if (thresholdIsMin.isSelected() + && aboveThreshold != AnnotationColourGradient.NO_THRESHOLD) { acg.setAutoScaled(false); - if (aboveThreshold==AnnotationColourGradient.ABOVE_THRESHOLD) - { + if (aboveThreshold == AnnotationColourGradient.ABOVE_THRESHOLD) + { acg = new GraduatedColor(acg, threshline.value, max); - } else { - acg = new GraduatedColor(acg, min,threshline.value); } - } else { + else + { + acg = new GraduatedColor(acg, min, threshline.value); + } + } + else + { acg.setAutoScaled(true); } - - fr.featureColours.put(type,acg); + acg.setColourByLabel(colourByLabel.isSelected()); + if (acg.isColourByLabel()) + { + maxColour.setEnabled(false); + minColour.setEnabled(false); + maxColour.setBackground(this.getBackground()); + maxColour.setForeground(this.getBackground()); + minColour.setBackground(this.getBackground()); + minColour.setForeground(this.getBackground()); + + } + else + { + maxColour.setEnabled(true); + minColour.setEnabled(true); + maxColour.setBackground(oldmaxColour); + minColour.setBackground(oldminColour); + maxColour.setForeground(oldmaxColour); + minColour.setForeground(oldminColour); + } + fr.featureColours.put(type, acg); cs = acg; ap.paintAlignment(false); } - public void ok_actionPerformed(ActionEvent e) + protected void raiseClosed() { - changeColour(); - try - { - frame.setClosed(true); - } catch (Exception ex) + if (this.colourEditor != null) { + colourEditor.actionPerformed(new ActionEvent(this, 0, "CLOSED")); } } - public void cancel_actionPerformed(ActionEvent e) + public void okPressed() + { + changeColour(); + } + + + public void cancelPressed() { reset(); - try - { - frame.setClosed(true); - } catch (Exception ex) - { - } } void reset() { fr.featureColours.put(type, oldcs); + ap.paintAlignment(false); + cs = null; } public void thresholdCheck_actionPerformed(ActionEvent e) @@ -451,22 +520,26 @@ public class FeatureColourChooser extends JPanel ap.paintAlignment(false); } - public void currentColours_actionPerformed(ActionEvent e) + public void thresholdIsMin_actionPerformed(ActionEvent actionEvent) { - if (currentColours.isSelected()) - { - reset(); - } - - maxColour.setEnabled(!currentColours.isSelected()); - minColour.setEnabled(!currentColours.isSelected()); - changeColour(); } - public void thresholdIsMin_actionPerformed(ActionEvent actionEvent) + public void colourByLabel_actionPerformed(ActionEvent actionEvent) { changeColour(); } + ActionListener colourEditor = null; + + public void addActionListener(ActionListener graduatedColorEditor) + { + if (colourEditor != null) + { + System.err + .println("IMPLEMENTATION ISSUE: overwriting action listener for FeatureColourChooser"); + } + colourEditor = graduatedColorEditor; + } + }