X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationColourChooser.java;h=7fb868fcd829f6b42efb0fc081b6f1fcc01d339d;hb=e010226a8f1496347788042a68131ee97224d0b3;hp=a05ccf134d5943704c4b10c52a8b368a40849bae;hpb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;p=jalview.git diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java index a05ccf1..7fb868f 100755 --- a/src/jalview/gui/AnnotationColourChooser.java +++ b/src/jalview/gui/AnnotationColourChooser.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, 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 file is part of Jalview. * @@ -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; @@ -47,10 +51,10 @@ public class AnnotationColourChooser extends JPanel 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(); + Vector allGroups = ap.av.getAlignment().getGroups(); SequenceGroup sg; for (int g = 0; g < allGroups.size(); g++) { @@ -66,7 +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() { @@ -87,29 +91,31 @@ public class AnnotationColourChooser extends JPanel } }); - 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()); + } } adjusting = true; Vector list = new Vector(); int index = 1; - for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++) + for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++) { - String label = av.alignment.getAlignmentAnnotation()[i].label; + String label = av.getAlignment().getAlignmentAnnotation()[i].label; if (!list.contains(label)) list.addElement(label); else @@ -122,6 +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(); @@ -132,9 +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 @@ -148,7 +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"); @@ -162,7 +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"); @@ -194,8 +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) @@ -203,8 +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) @@ -212,7 +255,6 @@ public class AnnotationColourChooser extends JPanel threshold_actionPerformed(e); } }); - jPanel3.setLayout(flowLayout2); thresholdValue.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -228,8 +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() @@ -240,6 +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() { @@ -248,19 +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; @@ -268,24 +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(); @@ -327,7 +378,7 @@ public class AnnotationColourChooser extends JPanel return; } - currentAnnotation = av.alignment.getAlignmentAnnotation()[annotations + currentAnnotation = av.getAlignment().getAlignmentAnnotation()[annotations .getSelectedIndex()]; int aboveThreshold = -1; @@ -342,12 +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) @@ -397,9 +450,9 @@ public class AnnotationColourChooser extends JPanel av.setGlobalColourScheme(acg); - if (av.alignment.getGroups() != null) + if (av.getAlignment().getGroups() != null) { - Vector allGroups = ap.av.alignment.getGroups(); + Vector allGroups = ap.av.getAlignment().getGroups(); SequenceGroup sg; for (int g = 0; g < allGroups.size(); g++) { @@ -424,8 +477,8 @@ public class AnnotationColourChooser extends JPanel } } - - 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); @@ -453,9 +508,9 @@ 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(); + Vector allGroups = ap.av.getAlignment().getGroups(); SequenceGroup sg; for (int g = 0; g < allGroups.size(); g++) {