X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationColourChooser.java;h=9df3b731e4cc30af7cdef33e1f3155e780570bc4;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=4416ec34525ad64c4795f37f5e9a5609b6d22a7d;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/appletgui/AnnotationColourChooser.java b/src/jalview/appletgui/AnnotationColourChooser.java old mode 100755 new mode 100644 index 4416ec3..9df3b73 --- a/src/jalview/appletgui/AnnotationColourChooser.java +++ b/src/jalview/appletgui/AnnotationColourChooser.java @@ -1,31 +1,52 @@ /* - * 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 2.9) + * Copyright (C) 2015 The Jalview Authors * - * 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. + * + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.appletgui; -import java.util.*; - -import java.awt.*; -import java.awt.event.*; - -import jalview.datamodel.*; -import jalview.schemes.*; -import java.awt.Rectangle; +import jalview.datamodel.SequenceGroup; +import jalview.schemes.AnnotationColourGradient; +import jalview.schemes.ColourSchemeI; +import jalview.util.MessageManager; + +import java.awt.BorderLayout; +import java.awt.Button; +import java.awt.Checkbox; +import java.awt.Choice; +import java.awt.Color; +import java.awt.Dimension; +import java.awt.FlowLayout; +import java.awt.Font; +import java.awt.Frame; +import java.awt.Panel; +import java.awt.Scrollbar; +import java.awt.TextField; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.AdjustmentEvent; +import java.awt.event.AdjustmentListener; +import java.awt.event.ItemEvent; +import java.awt.event.ItemListener; +import java.awt.event.MouseEvent; +import java.awt.event.MouseListener; +import java.util.Hashtable; +import java.util.Vector; public class AnnotationColourChooser extends Panel implements ActionListener, AdjustmentListener, ItemListener, MouseListener @@ -54,14 +75,11 @@ public class AnnotationColourChooser extends Panel implements } 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.elementAt(g); if (sg.cs != null) { oldgroupColours.put(sg, sg.cs); @@ -78,34 +96,40 @@ public class AnnotationColourChooser extends Panel implements slider.addAdjustmentListener(this); slider.addMouseListener(this); - if (av.alignment.getAlignmentAnnotation() == null) + if (av.getAlignment().getAlignmentAnnotation() == null) { return; } + setDefaultMinMax(); + + adjusting = true; 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.setState(acg.isPredefinedColours() + || acg.getBaseColour() != null); + if (!acg.isPredefinedColours() && acg.getBaseColour() == null) + { + minColour.setBackground(acg.getMinColour()); + maxColour.setBackground(acg.getMaxColour()); + } + // seqAssociated.setState(acg.isSeqAssociated()); } - 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 + { list.addElement(label + "_" + (index++)); + } } for (int i = 0; i < list.size(); i++) @@ -113,9 +137,36 @@ public class AnnotationColourChooser extends Panel implements annotations.addItem(list.elementAt(i).toString()); } - threshold.addItem("No Threshold"); - threshold.addItem("Above Threshold"); - threshold.addItem("Below Threshold"); + threshold.addItem(MessageManager + .getString("label.threshold_feature_no_thereshold")); + threshold.addItem(MessageManager + .getString("label.threshold_feature_above_thereshold")); + threshold.addItem(MessageManager + .getString("label.threshold_feature_below_thereshold")); + + if (oldcs instanceof AnnotationColourGradient) + { + AnnotationColourGradient acg = (AnnotationColourGradient) oldcs; + annotations.select(acg.getAnnotation()); + switch (acg.getAboveThreshold()) + { + case AnnotationColourGradient.NO_THRESHOLD: + threshold.select(0); + break; + case AnnotationColourGradient.ABOVE_THRESHOLD: + threshold.select(1); + break; + case AnnotationColourGradient.BELOW_THRESHOLD: + threshold.select(1); + break; + default: + throw new Error( + MessageManager + .getString("error.implementation_error_dont_know_thereshold_annotationcolourgradient")); + } + thresholdIsMin.setState(acg.thresholdIsMinMax); + thresholdValue.setText("" + acg.getAnnotationThreshold()); + } adjusting = false; @@ -123,11 +174,21 @@ public class AnnotationColourChooser extends Panel implements frame = new Frame(); frame.add(this); - jalview.bin.JalviewLite.addFrame(frame, "Colour by Annotation", 480, - 145); + jalview.bin.JalviewLite.addFrame(frame, + MessageManager.getString("label.colour_by_annotation"), 560, + 175); validate(); } + private void setDefaultMinMax() + { + minColour.setBackground(av.applet.getDefaultColourParameter( + "ANNOTATIONCOLOUR_MIN", Color.orange)); + maxColour.setBackground(av.applet.getDefaultColourParameter( + "ANNOTATIONCOLOUR_MAX", Color.red)); + + } + public AnnotationColourChooser() { try @@ -142,58 +203,78 @@ public class AnnotationColourChooser extends Panel implements private void jbInit() throws Exception { minColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - minColour.setLabel("Min Colour"); + minColour.setLabel(MessageManager.getString("label.min_colour")); minColour.addActionListener(this); maxColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - maxColour.setLabel("Max Colour"); + maxColour.setLabel(MessageManager.getString("label.max_colour")); maxColour.addActionListener(this); thresholdIsMin.addItemListener(this); - ok.setLabel("OK"); + ok.setLabel(MessageManager.getString("action.ok")); ok.addActionListener(this); - cancel.setLabel("Cancel"); + cancel.setLabel(MessageManager.getString("action.cancel")); cancel.addActionListener(this); - this.setLayout(borderLayout1); - jPanel2.setLayout(flowLayout1); + defColours.setLabel(MessageManager.getString("action.set_defaults")); + defColours.addActionListener(this); + annotations.addItemListener(this); - jPanel1.setBackground(Color.white); - jPanel2.setBackground(Color.white); - threshold.addItemListener(this); - jPanel3.setLayout(null); thresholdValue.addActionListener(this); - slider.setBackground(Color.white); + slider.setPreferredSize(new Dimension(193, 21)); slider.setEnabled(false); - slider.setBounds(new Rectangle(153, 3, 93, 21)); + thresholdValue.setPreferredSize(new Dimension(79, 22)); thresholdValue.setEnabled(false); - thresholdValue.setBounds(new Rectangle(248, 2, 79, 22)); thresholdValue.setColumns(5); - jPanel3.setBackground(Color.white); currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - currentColours.setLabel("Use Original Colours"); + currentColours.setLabel(MessageManager + .getString("label.use_original_colours")); currentColours.addItemListener(this); - threshold.setBounds(new Rectangle(11, 3, 139, 22)); thresholdIsMin.setBackground(Color.white); - thresholdIsMin.setLabel("Threshold is min/max"); - thresholdIsMin.setBounds(new Rectangle(328, 3, 135, 23)); + thresholdIsMin.setLabel(MessageManager + .getString("label.threshold_minmax")); + + this.setLayout(borderLayout1); + + jPanel1.setBackground(Color.white); + + jPanel2.setLayout(new FlowLayout()); + jPanel2.setBackground(Color.white); + threshold.addItemListener(this); + jPanel3.setLayout(new FlowLayout()); + jPanel3.setBackground(Color.white); + Panel jPanel4 = new Panel(); + jPanel4.setLayout(new BorderLayout()); + jPanel4.setBackground(Color.white); + jPanel1.add(ok); jPanel1.add(cancel); + jPanel2.add(annotations); jPanel2.add(currentColours); jPanel2.add(minColour); jPanel2.add(maxColour); - jPanel3.add(threshold); - jPanel3.add(slider); - jPanel3.add(thresholdValue); - jPanel3.add(thresholdIsMin); - this.add(jPanel2, java.awt.BorderLayout.NORTH); - this.add(jPanel3, java.awt.BorderLayout.CENTER); + + jPanel4.add(thresholdIsMin, BorderLayout.WEST); + jPanel4.add(slider, BorderLayout.CENTER); + jPanel4.add(thresholdValue, BorderLayout.EAST); + + Panel jPanel34 = new Panel(); + jPanel34.setLayout(new BorderLayout()); + jPanel34.setBackground(Color.white); + jPanel34.add(jPanel2, BorderLayout.NORTH); + jPanel34.add(threshold, BorderLayout.WEST); + jPanel3.add(defColours); + jPanel34.add(jPanel3, BorderLayout.EAST); + jPanel34.add(jPanel4, BorderLayout.SOUTH); + + this.add(jPanel34, java.awt.BorderLayout.CENTER); this.add(jPanel1, java.awt.BorderLayout.SOUTH); + } Choice annotations = new Choice(); @@ -206,6 +287,8 @@ public class AnnotationColourChooser extends Panel implements Button cancel = new Button(); + Button defColours = new Button(); + Panel jPanel1 = new Panel(); Panel jPanel2 = new Panel(); @@ -247,10 +330,12 @@ public class AnnotationColourChooser extends Panel implements { maxColour_actionPerformed(null); } - + else if (evt.getSource() == defColours) + { + defColour_actionPerformed(); + } else if (evt.getSource() == ok) { - changeColour(); frame.setVisible(false); } else if (evt.getSource() == cancel) @@ -287,14 +372,14 @@ public class AnnotationColourChooser extends Panel implements { if (!adjusting) { - thresholdValue.setText(((float) slider.getValue() / 1000f) + ""); + thresholdValue.setText((slider.getValue() / 1000f) + ""); if (currentColours.getState() && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient)) { changeColour(); } - currentAnnotation.threshold.value = (float) slider.getValue() / 1000f; + currentAnnotation.threshold.value = slider.getValue() / 1000f; ap.paintAlignment(false); } } @@ -328,6 +413,14 @@ public class AnnotationColourChooser extends Panel implements } } + public void defColour_actionPerformed() + { + setDefaultMinMax(); + minColour.repaint(); + maxColour.repaint(); + changeColour(); + } + void changeColour() { // Check if combobox is still adjusting @@ -336,26 +429,28 @@ public class AnnotationColourChooser extends Panel implements return; } - currentAnnotation = av.alignment.getAlignmentAnnotation()[annotations + currentAnnotation = av.getAlignment().getAlignmentAnnotation()[annotations .getSelectedIndex()]; int aboveThreshold = -1; - if (threshold.getSelectedItem().equals("Above Threshold")) + if (threshold.getSelectedIndex() == 1) { aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD; } - else if (threshold.getSelectedItem().equals("Below Threshold")) + else if (threshold.getSelectedIndex() == 2) { aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD; } slider.setEnabled(true); thresholdValue.setEnabled(true); + thresholdIsMin.setEnabled(true); if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD) { slider.setEnabled(false); thresholdValue.setEnabled(false); + thresholdIsMin.setEnabled(false); thresholdValue.setText(""); } else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD @@ -383,32 +478,31 @@ public class AnnotationColourChooser extends Panel implements AnnotationColourGradient acg = null; if (currentColours.getState()) { - 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 && currentAnnotation.graphMax == 0f) { - acg.predefinedColours = true; + acg.setPredefinedColours(true); } acg.thresholdIsMinMax = thresholdIsMin.getState(); av.setGlobalColourScheme(acg); - if (av.alignment.getGroups() != null) + // TODO: per group colour propagation not always desired + 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.elementAt(g); if (sg.cs == null) { @@ -422,27 +516,26 @@ public class AnnotationColourChooser extends Panel implements } else { - sg.cs = new AnnotationColourGradient(currentAnnotation, minColour - .getBackground(), maxColour.getBackground(), + sg.cs = new AnnotationColourGradient(currentAnnotation, + minColour.getBackground(), maxColour.getBackground(), aboveThreshold); } } } - ap.paintAlignment(false); + // update colours in linked windows + ap.alignmentChanged(); + ap.paintAlignment(true); } 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.elementAt(g); Object cs = oldgroupColours.get(sg); if (cs instanceof ColourSchemeI) {