X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationColourChooser.java;h=3c0f704e48fe37b868c6607fd797142bc98c2672;hb=6235128370382f0fecdf3ba1cc683052c5aa11e7;hp=1a661be1e4bc9e4d9716c700180d61800e8860c0;hpb=b81d4d7d46ea8b1c89df086fb847baab6b69d427;p=jalview.git diff --git a/src/jalview/appletgui/AnnotationColourChooser.java b/src/jalview/appletgui/AnnotationColourChooser.java old mode 100755 new mode 100644 index 1a661be..3c0f704 --- a/src/jalview/appletgui/AnnotationColourChooser.java +++ b/src/jalview/appletgui/AnnotationColourChooser.java @@ -1,13 +1,13 @@ /* - * 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 + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8) + * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle * * 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 @@ -24,9 +24,7 @@ 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 @@ -58,7 +56,7 @@ public class AnnotationColourChooser extends Panel implements if (av.getAlignment().getGroups() != null) { oldgroupColours = new Hashtable(); - for (SequenceGroup sg: ap.av.getAlignment().getGroups()) + for (SequenceGroup sg : ap.av.getAlignment().getGroups()) { if (sg.cs != null) { @@ -82,18 +80,20 @@ public class AnnotationColourChooser extends Panel implements } 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; @@ -119,21 +119,23 @@ public class AnnotationColourChooser extends Panel implements { AnnotationColourGradient acg = (AnnotationColourGradient) oldcs; annotations.select(acg.getAnnotation()); - switch (acg.getAboveThreshold()) { + switch (acg.getAboveThreshold()) + { case AnnotationColourGradient.NO_THRESHOLD: - threshold.select("No Threshold"); + threshold.select("No Threshold"); break; case AnnotationColourGradient.ABOVE_THRESHOLD: - threshold.select("Above Threshold"); + threshold.select("Above Threshold"); break; case AnnotationColourGradient.BELOW_THRESHOLD: threshold.select("Below Threshold"); 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; @@ -142,17 +144,20 @@ 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 @@ -167,43 +172,43 @@ 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); @@ -213,32 +218,30 @@ 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(); @@ -250,7 +253,7 @@ public class AnnotationColourChooser extends Panel implements Button ok = new Button(); Button cancel = new Button(); - + Button defColours = new Button(); Panel jPanel1 = new Panel(); @@ -296,7 +299,7 @@ public class AnnotationColourChooser extends Panel implements } else if (evt.getSource() == defColours) { - defColour_actionPerformed(); + defColour_actionPerformed(); } else if (evt.getSource() == ok) { @@ -377,6 +380,7 @@ public class AnnotationColourChooser extends Panel implements new UserDefinedColours(this, "Max Colour", maxColour.getBackground()); } } + public void defColour_actionPerformed() { setDefaultMinMax(); @@ -384,6 +388,7 @@ public class AnnotationColourChooser extends Panel implements maxColour.repaint(); changeColour(); } + void changeColour() { // Check if combobox is still adjusting @@ -454,18 +459,19 @@ 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); + // TODO: per group colour propagation not always desired if (av.getAlignment().getGroups() != null) { - for (SequenceGroup sg:ap.av.getAlignment().getGroups()) + for (SequenceGroup sg : ap.av.getAlignment().getGroups()) { - + if (sg.cs == null) { continue; @@ -487,6 +493,7 @@ public class AnnotationColourChooser extends Panel implements } // update colours in linked windows + ap.alignmentChanged(); ap.paintAlignment(true); } @@ -495,7 +502,7 @@ public class AnnotationColourChooser extends Panel implements av.setGlobalColourScheme(oldcs); if (av.getAlignment().getGroups() != null) { - for (SequenceGroup sg:ap.av.getAlignment().getGroups()) + for (SequenceGroup sg : ap.av.getAlignment().getGroups()) { Object cs = oldgroupColours.get(sg); if (cs instanceof ColourSchemeI)