X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationColourChooser.java;h=3e7a3fd18c0819d2a5dc484bde0b8f25a5835b70;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=1e9668a11183445c18cee116831c3b43e4521036;hpb=87358521afabb1f5382a1fff5f991149c838b1e2;p=jalview.git diff --git a/src/jalview/appletgui/AnnotationColourChooser.java b/src/jalview/appletgui/AnnotationColourChooser.java old mode 100755 new mode 100644 index 1e9668a..3e7a3fd --- a/src/jalview/appletgui/AnnotationColourChooser.java +++ b/src/jalview/appletgui/AnnotationColourChooser.java @@ -1,19 +1,20 @@ /* - * 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 2.8.2) + * Copyright (C) 2014 The Jalview Authors * * 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 * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.appletgui; @@ -24,9 +25,7 @@ import java.awt.event.*; import jalview.datamodel.*; import jalview.schemes.*; -import java.awt.Rectangle; - -import javax.swing.BoxLayout; +import jalview.util.MessageManager; public class AnnotationColourChooser extends Panel implements ActionListener, AdjustmentListener, ItemListener, MouseListener @@ -55,14 +54,11 @@ 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); @@ -79,30 +75,32 @@ 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; - currentColours.setState(acg.predefinedColours); - if (!acg.predefinedColours) { + 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 @@ -114,29 +112,31 @@ 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()) { + switch (acg.getAboveThreshold()) + { case AnnotationColourGradient.NO_THRESHOLD: - threshold.select("No Threshold"); + threshold.select(0); break; case AnnotationColourGradient.ABOVE_THRESHOLD: - threshold.select("Above Threshold"); + threshold.select(1); break; case AnnotationColourGradient.BELOW_THRESHOLD: - threshold.select("Below Threshold"); + threshold.select(1); break; - default: - throw new Error("Implementation error: don't know about threshold setting for current AnnotationColourGradient."); + default: + throw new Error( + "Implementation error: don't know about threshold setting for current AnnotationColourGradient."); } thresholdIsMin.setState(acg.thresholdIsMinMax); - thresholdValue.setText(""+acg.getAnnotationThreshold()); + thresholdValue.setText("" + acg.getAnnotationThreshold()); } adjusting = false; @@ -145,17 +145,20 @@ public class AnnotationColourChooser extends Panel implements frame = new Frame(); frame.add(this); - jalview.bin.JalviewLite.addFrame(frame, "Colour by Annotation", 560, + 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)); + minColour.setBackground(av.applet.getDefaultColourParameter( + "ANNOTATIONCOLOUR_MIN", Color.orange)); + maxColour.setBackground(av.applet.getDefaultColourParameter( + "ANNOTATIONCOLOUR_MAX", Color.red)); } + public AnnotationColourChooser() { try @@ -170,43 +173,43 @@ 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); - defColours.setLabel("Defaults"); + defColours.setLabel(MessageManager.getString("action.set_defaults")); defColours.addActionListener(this); - + annotations.addItemListener(this); thresholdValue.addActionListener(this); slider.setBackground(Color.white); - slider.setPreferredSize(new Dimension(193,21)); + slider.setPreferredSize(new Dimension(193, 21)); slider.setEnabled(false); - thresholdValue.setPreferredSize(new Dimension(79,22)); + thresholdValue.setPreferredSize(new Dimension(79, 22)); thresholdValue.setEnabled(false); thresholdValue.setColumns(5); 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); thresholdIsMin.setBackground(Color.white); - thresholdIsMin.setLabel("Threshold is min/max"); + 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); @@ -216,32 +219,30 @@ public class AnnotationColourChooser extends Panel implements 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); - - + 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(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(); @@ -253,7 +254,7 @@ public class AnnotationColourChooser extends Panel implements Button ok = new Button(); Button cancel = new Button(); - + Button defColours = new Button(); Panel jPanel1 = new Panel(); @@ -299,7 +300,7 @@ public class AnnotationColourChooser extends Panel implements } else if (evt.getSource() == defColours) { - defColour_actionPerformed(); + defColour_actionPerformed(); } else if (evt.getSource() == ok) { @@ -380,6 +381,7 @@ public class AnnotationColourChooser extends Panel implements new UserDefinedColours(this, "Max Colour", maxColour.getBackground()); } } + public void defColour_actionPerformed() { setDefaultMinMax(); @@ -387,6 +389,7 @@ public class AnnotationColourChooser extends Panel implements maxColour.repaint(); changeColour(); } + void changeColour() { // Check if combobox is still adjusting @@ -395,15 +398,15 @@ 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; } @@ -457,20 +460,18 @@ public class AnnotationColourChooser extends Panel implements 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) { @@ -493,19 +494,17 @@ public class AnnotationColourChooser extends Panel implements } // 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) {