X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationColourChooser.java;h=1a661be1e4bc9e4d9716c700180d61800e8860c0;hb=b81d4d7d46ea8b1c89df086fb847baab6b69d427;hp=41c20bdd90ff48e49f327bbf0dca9da0071e8cdc;hpb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;p=jalview.git diff --git a/src/jalview/appletgui/AnnotationColourChooser.java b/src/jalview/appletgui/AnnotationColourChooser.java index 41c20bd..1a661be 100755 --- a/src/jalview/appletgui/AnnotationColourChooser.java +++ b/src/jalview/appletgui/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. * @@ -26,6 +26,8 @@ import jalview.datamodel.*; import jalview.schemes.*; import java.awt.Rectangle; +import javax.swing.BoxLayout; + public class AnnotationColourChooser extends Panel implements ActionListener, AdjustmentListener, ItemListener, MouseListener { @@ -53,14 +55,11 @@ 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); @@ -77,30 +76,30 @@ public class AnnotationColourChooser extends Panel implements slider.addAdjustmentListener(this); slider.addMouseListener(this); - if (av.alignment.getAlignmentAnnotation() == null) + if (av.getAlignment().getAlignmentAnnotation() == null) { return; } + 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.setState(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 @@ -116,17 +115,44 @@ public class AnnotationColourChooser extends Panel implements threshold.addItem("Above Threshold"); threshold.addItem("Below Threshold"); + if (oldcs instanceof AnnotationColourGradient) + { + AnnotationColourGradient acg = (AnnotationColourGradient) oldcs; + annotations.select(acg.getAnnotation()); + switch (acg.getAboveThreshold()) { + case AnnotationColourGradient.NO_THRESHOLD: + threshold.select("No Threshold"); + break; + case AnnotationColourGradient.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."); + } + thresholdIsMin.setState(acg.thresholdIsMinMax); + thresholdValue.setText(""+acg.getAnnotationThreshold()); + } + adjusting = false; changeColour(); frame = new Frame(); frame.add(this); - jalview.bin.JalviewLite.addFrame(frame, "Colour by Annotation", 480, - 145); + jalview.bin.JalviewLite.addFrame(frame, "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 @@ -155,44 +181,64 @@ public class AnnotationColourChooser extends Panel implements cancel.setLabel("Cancel"); cancel.addActionListener(this); - this.setLayout(borderLayout1); - jPanel2.setLayout(flowLayout1); + defColours.setLabel("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.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)); + + 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(); @@ -204,6 +250,8 @@ public class AnnotationColourChooser extends Panel implements Button ok = new Button(); Button cancel = new Button(); + + Button defColours = new Button(); Panel jPanel1 = new Panel(); @@ -246,7 +294,10 @@ public class AnnotationColourChooser extends Panel implements { maxColour_actionPerformed(null); } - + else if (evt.getSource() == defColours) + { + defColour_actionPerformed(); + } else if (evt.getSource() == ok) { changeColour(); @@ -326,7 +377,13 @@ public class AnnotationColourChooser extends Panel implements new UserDefinedColours(this, "Max Colour", maxColour.getBackground()); } } - + public void defColour_actionPerformed() + { + setDefaultMinMax(); + minColour.repaint(); + maxColour.repaint(); + changeColour(); + } void changeColour() { // Check if combobox is still adjusting @@ -335,7 +392,7 @@ public class AnnotationColourChooser extends Panel implements return; } - currentAnnotation = av.alignment.getAlignmentAnnotation()[annotations + currentAnnotation = av.getAlignment().getAlignmentAnnotation()[annotations .getSelectedIndex()]; int aboveThreshold = -1; @@ -350,11 +407,13 @@ public class AnnotationColourChooser extends Panel implements 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 @@ -402,14 +461,11 @@ public class AnnotationColourChooser extends Panel implements av.setGlobalColourScheme(acg); - 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); - + if (sg.cs == null) { continue; @@ -430,19 +486,17 @@ public class AnnotationColourChooser extends Panel implements } } - ap.paintAlignment(false); + // update colours in linked windows + 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) {