X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationColourChooser.java;h=2b9787ff8ecdfff12bd920b7b50a13f765653d95;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=1ed94615f2c8c5b91aaa6f4d14ccf5c193ae54ab;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java index 1ed9461..2b9787f 100755 --- a/src/jalview/gui/AnnotationColourChooser.java +++ b/src/jalview/gui/AnnotationColourChooser.java @@ -1,20 +1,19 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) - * Copyright (C) 2009 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; @@ -22,9 +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; @@ -67,7 +70,7 @@ 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() { @@ -93,16 +96,18 @@ public class AnnotationColourChooser extends JPanel 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()); + } } adjusting = true; @@ -123,6 +128,27 @@ public class AnnotationColourChooser extends JPanel 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(); @@ -133,9 +159,16 @@ public class AnnotationColourChooser extends JPanel adjusting = false; changeColour(); + validate(); } + private void setDefaultMinMax() + { + minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange)); + maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red)); + } + public AnnotationColourChooser() { try @@ -149,7 +182,7 @@ 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"); @@ -163,7 +196,7 @@ 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"); @@ -195,8 +228,19 @@ 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) @@ -204,8 +248,6 @@ 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) @@ -213,7 +255,6 @@ public class AnnotationColourChooser extends JPanel threshold_actionPerformed(e); } }); - jPanel3.setLayout(flowLayout2); thresholdValue.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -229,8 +270,7 @@ 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() @@ -241,6 +281,7 @@ public class AnnotationColourChooser extends JPanel } }); thresholdIsMin.setBackground(Color.white); + thresholdIsMin.setFont(JvSwingUtils.getLabelFont()); thresholdIsMin.setText("Threshold is Min/Max"); thresholdIsMin.addActionListener(new ActionListener() { @@ -249,19 +290,34 @@ public class AnnotationColourChooser extends JPanel thresholdIsMin_actionPerformed(actionEvent); } }); + 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(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); + } + + protected void resetColours_actionPerformed(ActionEvent arg0) + { + setDefaultMinMax(); + changeColour(); } JComboBox annotations; @@ -269,24 +325,18 @@ public class AnnotationColourChooser extends JPanel 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(); - FlowLayout flowLayout1 = new FlowLayout(); - - JPanel jPanel3 = new JPanel(); - - FlowLayout flowLayout2 = new FlowLayout(); JSlider slider = new JSlider(); @@ -343,12 +393,14 @@ 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) @@ -378,13 +430,14 @@ 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); } if (currentAnnotation.graphMin == 0f @@ -417,15 +470,15 @@ public class AnnotationColourChooser extends JPanel } else { - sg.cs = new AnnotationColourGradient(currentAnnotation, minColour - .getBackground(), maxColour.getBackground(), + sg.cs = new AnnotationColourGradient(currentAnnotation, + minColour.getBackground(), maxColour.getBackground(), aboveThreshold); } } } - - ap.paintAlignment(false); + // ensure all associated views (overviews, structures, etc) are notified of updated colours. + ap.paintAlignment(true); } public void ok_actionPerformed(ActionEvent e) @@ -442,6 +495,8 @@ 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);