From: gmungoc Date: Tue, 14 Feb 2017 12:34:54 +0000 (+0000) Subject: Merge branch 'develop' into bug/JAL-2346annotationChoice X-Git-Tag: Release_2_10_3b1~336^2~2^2~1^2~2^2~6 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=88f7d0a53dc11d3b23148fe0866b502b4b53b0e9;hp=c00cfcb9f2223f1225fba57e5de85141cfa4570c;p=jalview.git Merge branch 'develop' into bug/JAL-2346annotationChoice Conflicts: src/jalview/appletgui/AnnotationColourChooser.java src/jalview/gui/AnnotationRowFilter.java src/jalview/gui/Jalview2XML.java src/jalview/gui/PopupMenu.java src/jalview/schemes/AnnotationColourGradient.java --- diff --git a/src/jalview/appletgui/AnnotationColourChooser.java b/src/jalview/appletgui/AnnotationColourChooser.java index 487b75c..f516bc9 100644 --- a/src/jalview/appletgui/AnnotationColourChooser.java +++ b/src/jalview/appletgui/AnnotationColourChooser.java @@ -46,7 +46,8 @@ 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.HashMap; +import java.util.Map; import java.util.Vector; public class AnnotationColourChooser extends Panel implements @@ -60,9 +61,15 @@ public class AnnotationColourChooser extends Panel implements ColourSchemeI oldcs; - Hashtable oldgroupColours; + Map oldgroupColours; - jalview.datamodel.AlignmentAnnotation currentAnnotation; + /* + * map from annotation to its menu item display label + * - so we know which item to pre-select on restore + */ + private Map annotationLabels; + + AlignmentAnnotation currentAnnotation; boolean adjusting = false; @@ -78,17 +85,10 @@ public class AnnotationColourChooser extends Panel implements oldcs = av.getGlobalColourScheme(); if (av.getAlignment().getGroups() != null) { - oldgroupColours = new Hashtable(); + oldgroupColours = new HashMap(); for (SequenceGroup sg : ap.av.getAlignment().getGroups()) { - if (sg.getColourScheme() != null) - { - oldgroupColours.put(sg, sg.getColourScheme()); - } - else - { - oldgroupColours.put(sg, "null"); - } + oldgroupColours.put(sg, sg.getColourScheme()); } } this.av = av; @@ -119,24 +119,7 @@ public class AnnotationColourChooser extends Panel implements // seqAssociated.setState(acg.isSeqAssociated()); } - Vector list = new Vector(); - int index = 1; - for (int i = 0; i < anns.length; i++) - { - String label = anns[i].label; - if (anns[i].sequenceRef != null) - { - label = label + "_" + anns[i].sequenceRef.getName(); - } - if (!list.contains(label)) - { - list.addElement(label); - } - else - { - list.addElement(label + "_" + (index++)); - } - } + Vector list = getAnnotationItems(); for (int i = 0; i < list.size(); i++) { @@ -153,7 +136,8 @@ public class AnnotationColourChooser extends Panel implements if (oldcs instanceof AnnotationColourGradient) { AnnotationColourGradient acg = (AnnotationColourGradient) oldcs; - annotations.select(acg.getAnnotation()); + String label = annotationLabels.get(acg.getAnnotation()); + annotations.select(label); switch (acg.getAboveThreshold()) { case AnnotationColourGradient.NO_THRESHOLD: @@ -170,7 +154,7 @@ public class AnnotationColourChooser extends Panel implements MessageManager .getString("error.implementation_error_dont_know_threshold_annotationcolourgradient")); } - thresholdIsMin.setState(acg.thresholdIsMinMax); + thresholdIsMin.setState(acg.isThresholdIsMinMax()); thresholdValue.setText("" + acg.getAnnotationThreshold()); } @@ -186,6 +170,51 @@ public class AnnotationColourChooser extends Panel implements validate(); } + /** + * Builds and returns a list of menu items (display text) for choice of + * annotation. Also builds a map between annotations and their display labels. + * + * @return + */ + protected Vector getAnnotationItems() + { + // TODO remove duplication with gui.AnnotationRowFilter + // TODO add 'per sequence only' option / parameter + + annotationLabels = new HashMap(); + Vector list = new Vector(); + AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation(); + if (anns == null) + { + return list; + } + int index = 1; + for (int i = 0; i < anns.length; i++) + { + String label = anns[i].label; + if (anns[i].sequenceRef != null) + { + /* + * be helpful and include sequence id in label for + * sequence-associated annotation (JAL-2236) + */ + label = label + "_" + anns[i].sequenceRef.getName(); + } + if (!list.contains(label)) + { + list.addElement(label); + annotationLabels.put(anns[i], label); + } + else + { + label = label + "_" + (index++); + list.addElement(label); + annotationLabels.put(anns[i], label); + } + } + return list; + } + private void setDefaultMinMax() { minColour.setBackground(av.applet.getDefaultColourParameter( @@ -501,7 +530,7 @@ public class AnnotationColourChooser extends Panel implements acg.setPredefinedColours(true); } - acg.thresholdIsMinMax = thresholdIsMin.getState(); + acg.setThresholdIsMinMax(thresholdIsMin.getState()); av.setGlobalColourScheme(acg); @@ -510,7 +539,6 @@ public class AnnotationColourChooser extends Panel implements { for (SequenceGroup sg : ap.av.getAlignment().getGroups()) { - if (sg.getColourScheme() == null) { continue; @@ -527,7 +555,6 @@ public class AnnotationColourChooser extends Panel implements currentAnnotation, minColour.getBackground(), maxColour .getBackground(), aboveThreshold)); } - } } @@ -543,20 +570,10 @@ public class AnnotationColourChooser extends Panel implements { for (SequenceGroup sg : ap.av.getAlignment().getGroups()) { - Object cs = oldgroupColours.get(sg); - if (cs instanceof ColourSchemeI) - { - sg.setColourScheme((ColourSchemeI) cs); - } - else - { - // probably the "null" string we set it to if it was null originally. - sg.setColourScheme(null); - } + sg.setColourScheme(oldgroupColours.get(sg)); } } ap.paintAlignment(true); - } @Override diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java index 05688cb..c6266b2 100755 --- a/src/jalview/datamodel/AlignmentAnnotation.java +++ b/src/jalview/datamodel/AlignmentAnnotation.java @@ -20,10 +20,6 @@ */ package jalview.datamodel; -import jalview.analysis.Rna; -import jalview.analysis.SecStrConsensus.SimpleBP; -import jalview.analysis.WUSSParseException; - import java.util.Collection; import java.util.Collections; import java.util.HashMap; @@ -32,6 +28,10 @@ import java.util.List; import java.util.Map; import java.util.Map.Entry; +import jalview.analysis.Rna; +import jalview.analysis.SecStrConsensus.SimpleBP; +import jalview.analysis.WUSSParseException; + /** * DOCUMENT ME! * @@ -863,6 +863,10 @@ public class AlignmentAnnotation @Override public String toString() { + if (annotations == null) + { + return ""; + } StringBuilder buffer = new StringBuilder(256); for (int i = 0; i < annotations.length; i++) diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java index f6352d7..33f7ad0 100644 --- a/src/jalview/gui/AnnotationColourChooser.java +++ b/src/jalview/gui/AnnotationColourChooser.java @@ -21,6 +21,8 @@ package jalview.gui; import jalview.bin.Cache; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.GraphLine; import jalview.datamodel.SequenceGroup; import jalview.schemes.AnnotationColourGradient; import jalview.schemes.ColourSchemeI; @@ -35,9 +37,11 @@ import java.awt.event.ActionListener; import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; import java.util.Hashtable; +import java.util.Vector; import javax.swing.BorderFactory; import javax.swing.JButton; +import javax.swing.JCheckBox; import javax.swing.JColorChooser; import javax.swing.JComboBox; import javax.swing.JInternalFrame; @@ -49,27 +53,21 @@ import net.miginfocom.swing.MigLayout; @SuppressWarnings("serial") public class AnnotationColourChooser extends AnnotationRowFilter { + private static final int ONETHOUSAND = 1000; - ColourSchemeI oldcs; + private ColourSchemeI oldcs; - Hashtable oldgroupColours; + private JButton defColours; - /** - * enabled if the user is dragging the slider - try to keep updates to a - * minimun - */ + private Hashtable oldgroupColours; - JComboBox annotations; + private JCheckBox currentColours = new JCheckBox(); - JButton defColours = new JButton(); + private JPanel minColour = new JPanel(); - JPanel jPanel1 = new JPanel(); + private JPanel maxColour = new JPanel(); - JPanel jPanel2 = new JPanel(); - - BorderLayout borderLayout1 = new BorderLayout(); - - private JComboBox threshold = new JComboBox(); + private JCheckBox thresholdIsMin = new JCheckBox(); public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap) { @@ -118,15 +116,17 @@ public class AnnotationColourChooser extends AnnotationRowFilter seqAssociated.setSelected(acg.isSeqAssociated()); } - annotations = new JComboBox( - getAnnotationItems(seqAssociated.isSelected())); + Vector annotItems = getAnnotationItems(seqAssociated + .isSelected()); + annotations = new JComboBox(annotItems); populateThresholdComboBox(threshold); if (oldcs instanceof AnnotationColourGradient) { AnnotationColourGradient acg = (AnnotationColourGradient) oldcs; - annotations.setSelectedItem(acg.getAnnotation()); + String label = getAnnotationMenuLabel(acg.getAnnotation()); + annotations.setSelectedItem(label); switch (acg.getAboveThreshold()) { case AnnotationColourGradient.NO_THRESHOLD: @@ -143,16 +143,11 @@ public class AnnotationColourChooser extends AnnotationRowFilter MessageManager .getString("error.implementation_error_dont_know_about_threshold_setting")); } - thresholdIsMin.setSelected(acg.thresholdIsMinMax); + thresholdIsMin.setSelected(acg.isThresholdIsMinMax()); thresholdValue.setText("" + acg.getAnnotationThreshold()); } - try - { - jbInit(); - } catch (Exception ex) - { - } + jbInit(); adjusting = false; updateView(); @@ -160,19 +155,11 @@ public class AnnotationColourChooser extends AnnotationRowFilter frame.pack(); } - public AnnotationColourChooser() + @Override + protected void jbInit() { - try - { - jbInit(); - } catch (Exception ex) - { - ex.printStackTrace(); - } - } + super.jbInit(); - private void jbInit() throws Exception - { minColour.setFont(JvSwingUtils.getLabelFont()); minColour.setBorder(BorderFactory.createEtchedBorder()); minColour.setPreferredSize(new Dimension(40, 20)); @@ -203,26 +190,8 @@ public class AnnotationColourChooser extends AnnotationRowFilter } } }); - ok.setOpaque(false); - ok.setText(MessageManager.getString("action.ok")); - ok.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - ok_actionPerformed(); - } - }); - cancel.setOpaque(false); - cancel.setText(MessageManager.getString("action.cancel")); - cancel.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - cancel_actionPerformed(); - } - }); + + defColours = new JButton(); defColours.setOpaque(false); defColours.setText(MessageManager.getString("action.set_defaults")); defColours.setToolTipText(MessageManager @@ -237,38 +206,6 @@ public class AnnotationColourChooser extends AnnotationRowFilter } }); - annotations.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - annotations_actionPerformed(); - } - }); - getThreshold().addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - threshold_actionPerformed(); - } - }); - thresholdValue.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - thresholdValue_actionPerformed(); - } - }); - slider.setPaintLabels(false); - slider.setPaintTicks(true); - slider.setBackground(Color.white); - slider.setEnabled(false); - slider.setOpaque(false); - slider.setPreferredSize(new Dimension(100, 32)); - thresholdValue.setEnabled(false); - thresholdValue.setColumns(7); currentColours.setFont(JvSwingUtils.getLabelFont()); currentColours.setOpaque(false); currentColours.setText(MessageManager @@ -307,7 +244,9 @@ public class AnnotationColourChooser extends AnnotationRowFilter } }); - this.setLayout(borderLayout1); + this.setLayout(new BorderLayout()); + JPanel jPanel1 = new JPanel(); + JPanel jPanel2 = new JPanel(); jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]")); jPanel1.setBackground(Color.white); jPanel2.setBackground(Color.white); @@ -403,16 +342,6 @@ public class AnnotationColourChooser extends AnnotationRowFilter } } - public JComboBox getThreshold() - { - return threshold; - } - - public void setThreshold(JComboBox threshold) - { - this.threshold = threshold; - } - public void currentColours_actionPerformed() { if (currentColours.isSelected()) @@ -455,7 +384,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter { getCurrentAnnotation() .setThreshold( - new jalview.datamodel.GraphLine( + new GraphLine( (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f, "Threshold", Color.black)); } @@ -463,19 +392,19 @@ public class AnnotationColourChooser extends AnnotationRowFilter if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD) { adjusting = true; - float range = getCurrentAnnotation().graphMax * 1000 - - getCurrentAnnotation().graphMin * 1000; + float range = getCurrentAnnotation().graphMax * ONETHOUSAND + - getCurrentAnnotation().graphMin * ONETHOUSAND; - slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000)); - slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000)); - slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000)); + slider.setMinimum((int) (getCurrentAnnotation().graphMin * ONETHOUSAND)); + slider.setMaximum((int) (getCurrentAnnotation().graphMax * ONETHOUSAND)); + slider.setValue((int) (getCurrentAnnotation().threshold.value * ONETHOUSAND)); thresholdValue.setText(getCurrentAnnotation().threshold.value + ""); slider.setMajorTickSpacing((int) (range / 10f)); slider.setEnabled(true); thresholdValue.setEnabled(true); adjusting = false; } - colorAlignmContaining(getCurrentAnnotation(), selectedThresholdItem); + colorAlignmentContaining(getCurrentAnnotation(), selectedThresholdItem); ap.alignmentChanged(); // ensure all associated views (overviews, structures, etc) are notified of @@ -483,4 +412,60 @@ public class AnnotationColourChooser extends AnnotationRowFilter ap.paintAlignment(true); } + protected boolean colorAlignmentContaining(AlignmentAnnotation currentAnn, int selectedThresholdOption) + { + + AnnotationColourGradient acg = null; + if (currentColours.isSelected()) + { + acg = new AnnotationColourGradient(currentAnn, + av.getGlobalColourScheme(), selectedThresholdOption); + } + else + { + acg = new AnnotationColourGradient(currentAnn, + minColour.getBackground(), maxColour.getBackground(), + selectedThresholdOption); + } + acg.setSeqAssociated(seqAssociated.isSelected()); + + if (currentAnn.graphMin == 0f && currentAnn.graphMax == 0f) + { + acg.setPredefinedColours(true); + } + + acg.setThresholdIsMinMax(thresholdIsMin.isSelected()); + + av.setGlobalColourScheme(acg); + + if (av.getAlignment().getGroups() != null) + { + + for (SequenceGroup sg : ap.av.getAlignment().getGroups()) + { + if (sg.cs == null) + { + continue; + } + + if (currentColours.isSelected()) + { + sg.setColourScheme(new AnnotationColourGradient(currentAnn, sg + .getColourScheme(), selectedThresholdOption)); + ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated + .isSelected()); + } + else + { + sg.setColourScheme(new AnnotationColourGradient(currentAnn, + minColour.getBackground(), maxColour.getBackground(), + selectedThresholdOption)); + ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated + .isSelected()); + } + } + } + return false; + } + } diff --git a/src/jalview/gui/AnnotationColumnChooser.java b/src/jalview/gui/AnnotationColumnChooser.java index 1290d70..637eb30 100644 --- a/src/jalview/gui/AnnotationColumnChooser.java +++ b/src/jalview/gui/AnnotationColumnChooser.java @@ -30,7 +30,6 @@ import jalview.viewmodel.annotationfilter.AnnotationFilterParameter; import java.awt.BorderLayout; import java.awt.CardLayout; import java.awt.Color; -import java.awt.Dimension; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.ItemEvent; @@ -55,28 +54,10 @@ import net.miginfocom.swing.MigLayout; public class AnnotationColumnChooser extends AnnotationRowFilter implements ItemListener { - - private JComboBox annotations; - - private JPanel actionPanel = new JPanel(); - - private JPanel thresholdPanel = new JPanel(); - private JPanel switchableViewsPanel = new JPanel(new CardLayout()); - private CardLayout switchableViewsLayout = (CardLayout) (switchableViewsPanel - .getLayout()); - - private JPanel noGraphFilterView = new JPanel(); - - private JPanel graphFilterView = new JPanel(); - private JPanel annotationComboBoxPanel = new JPanel(); - private BorderLayout borderLayout1 = new BorderLayout(); - - private JComboBox threshold = new JComboBox(); - private StructureFilterPanel gStructureFilterPanel; private StructureFilterPanel ngStructureFilterPanel; @@ -107,17 +88,6 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements private ColumnSelection oldColumnSelection; - public AnnotationColumnChooser() - { - try - { - jbInit(); - } catch (Exception ex) - { - ex.printStackTrace(); - } - } - public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap) { super(av, ap); @@ -169,72 +139,27 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements frame.pack(); } - private void jbInit() throws Exception + @Override + protected void jbInit() { - ok.setOpaque(false); - ok.setText(MessageManager.getString("action.ok")); - ok.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - ok_actionPerformed(); - } - }); - - cancel.setOpaque(false); - cancel.setText(MessageManager.getString("action.cancel")); - cancel.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - cancel_actionPerformed(); - } - }); - - annotations.addItemListener(this); - annotations.setToolTipText(MessageManager - .getString("info.select_annotation_row")); - threshold.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - threshold_actionPerformed(); - } - }); - - thresholdValue.setEnabled(false); - thresholdValue.setColumns(7); - thresholdValue.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - thresholdValue_actionPerformed(); - } - }); - - slider.setPaintLabels(false); - slider.setPaintTicks(true); - slider.setBackground(Color.white); - slider.setEnabled(false); - slider.setOpaque(false); - slider.setPreferredSize(new Dimension(100, 32)); + super.jbInit(); + JPanel thresholdPanel = new JPanel(); thresholdPanel.setBorder(new TitledBorder(MessageManager .getString("label.threshold_filter"))); thresholdPanel.setBackground(Color.white); thresholdPanel.setFont(JvSwingUtils.getLabelFont()); thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]")); + JPanel actionPanel = new JPanel(); actionPanel.setBackground(Color.white); actionPanel.setFont(JvSwingUtils.getLabelFont()); + JPanel graphFilterView = new JPanel(); graphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]")); graphFilterView.setBackground(Color.white); + JPanel noGraphFilterView = new JPanel(); noGraphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]")); noGraphFilterView.setBackground(Color.white); @@ -270,7 +195,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements switchableViewsPanel.add(graphFilterView, AnnotationColumnChooser.GRAPH_VIEW); - this.setLayout(borderLayout1); + this.setLayout(new BorderLayout()); this.add(annotationComboBoxPanel, java.awt.BorderLayout.PAGE_START); this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER); this.add(actionPanel, java.awt.BorderLayout.SOUTH); @@ -280,7 +205,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements this.validate(); } - public void updateThresholdPanelToolTip() + protected void updateThresholdPanelToolTip() { thresholdValue.setToolTipText(""); slider.setToolTipText(""); @@ -297,7 +222,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements } @Override - public void reset() + protected void reset() { if (this.getOldColumnSelection() != null) { @@ -338,26 +263,6 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements } } - public JComboBox getThreshold() - { - return threshold; - } - - public void setThreshold(JComboBox threshold) - { - this.threshold = threshold; - } - - public JComboBox getAnnotations() - { - return annotations; - } - - public void setAnnotations(JComboBox annotations) - { - this.annotations = annotations; - } - @Override public void updateView() { @@ -568,6 +473,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements selectedAnnotationChanged(); } + @Override public void selectedAnnotationChanged() { String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW; @@ -585,6 +491,8 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements ngFurtherActionPanel.syncState(); ngStructureFilterPanel.syncState(); + CardLayout switchableViewsLayout = (CardLayout) switchableViewsPanel + .getLayout(); switchableViewsLayout.show(switchableViewsPanel, currentView); updateView(); } diff --git a/src/jalview/gui/AnnotationRowFilter.java b/src/jalview/gui/AnnotationRowFilter.java index 166e1ad..c1dcee7 100644 --- a/src/jalview/gui/AnnotationRowFilter.java +++ b/src/jalview/gui/AnnotationRowFilter.java @@ -22,12 +22,21 @@ package jalview.gui; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.GraphLine; -import jalview.datamodel.SequenceGroup; import jalview.schemes.AnnotationColourGradient; import jalview.util.MessageManager; +import java.awt.Color; +import java.awt.Dimension; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.FocusAdapter; +import java.awt.event.FocusEvent; +import java.awt.event.ItemEvent; +import java.awt.event.ItemListener; import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; +import java.util.HashMap; +import java.util.Map; import java.util.Vector; import javax.swing.JButton; @@ -49,12 +58,8 @@ public abstract class AnnotationRowFilter extends JPanel protected int[] annmap; - protected boolean enableSeqAss = false; - - private AlignmentAnnotation currentAnnotation; - protected boolean adjusting = false; - + protected JCheckBox currentColours = new JCheckBox(); protected JPanel minColour = new JPanel(); @@ -81,6 +86,38 @@ public abstract class AnnotationRowFilter extends JPanel */ protected boolean sliderDragging = false; + protected JComboBox threshold = new JComboBox(); + + protected JComboBox annotations; + + /* + * map from annotation to its menu item display label + * - so we know which item to pre-select on restore + */ + private Map annotationLabels; + + private AlignmentAnnotation currentAnnotation; + + /** + * Constructor + * + * @param av + * @param ap + */ + public AnnotationRowFilter(AlignViewport av, final AlignmentPanel ap) + { + this.av = av; + this.ap = ap; + thresholdValue.addFocusListener(new FocusAdapter() + { + @Override + public void focusLost(FocusEvent e) + { + thresholdValue_actionPerformed(); + } + }); + } + protected void addSliderChangeListener() { @@ -130,25 +167,27 @@ public abstract class AnnotationRowFilter extends JPanel }); } - public AnnotationRowFilter(AlignViewport av, final AlignmentPanel ap) - { - this.av = av; - this.ap = ap; - } - - public AnnotationRowFilter() - { - - } - + /** + * Builds and returns a list of menu items (display text) for choice of + * annotation. Also builds maps between annotations, their positions in the + * list, and their display labels in the list. + * + * @param isSeqAssociated + * @return + */ public Vector getAnnotationItems(boolean isSeqAssociated) { + annotationLabels = new HashMap(); + Vector list = new Vector(); int index = 1; int[] anmap = new int[av.getAlignment().getAlignmentAnnotation().length]; + seqAssociated.setEnabled(false); for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++) { - if (av.getAlignment().getAlignmentAnnotation()[i].sequenceRef == null) + AlignmentAnnotation annotation = av.getAlignment() + .getAlignmentAnnotation()[i]; + if (annotation.sequenceRef == null) { if (isSeqAssociated) { @@ -157,30 +196,29 @@ public abstract class AnnotationRowFilter extends JPanel } else { - enableSeqAss = true; + seqAssociated.setEnabled(true); } - String label = av.getAlignment().getAlignmentAnnotation()[i].label; + String label = annotation.label; // add associated sequence ID if available - if (!isSeqAssociated - && av.getAlignment().getAlignmentAnnotation()[i].sequenceRef != null) + if (!isSeqAssociated && annotation.sequenceRef != null) { - label = label - + "_" - + av.getAlignment().getAlignmentAnnotation()[i].sequenceRef - .getName(); + label = label + "_" + annotation.sequenceRef.getName(); } // make label unique if (!list.contains(label)) { anmap[list.size()] = i; list.add(label); + annotationLabels.put(annotation, label); } else { if (!isSeqAssociated) { anmap[list.size()] = i; - list.add(label + "_" + (index++)); + label = label + "_" + (index++); + list.add(label); + annotationLabels.put(annotation, label); } } } @@ -203,11 +241,6 @@ public abstract class AnnotationRowFilter extends JPanel return selectedThresholdItem; } - public void modelChanged() - { - seqAssociated.setEnabled(enableSeqAss); - } - public void ok_actionPerformed() { try @@ -230,22 +263,22 @@ public abstract class AnnotationRowFilter extends JPanel } } - public void thresholdCheck_actionPerformed() + protected void thresholdCheck_actionPerformed() { updateView(); } - public void annotations_actionPerformed() + protected void selectedAnnotationChanged() { updateView(); } - public void threshold_actionPerformed() + protected void threshold_actionPerformed() { updateView(); } - public void thresholdValue_actionPerformed() + protected void thresholdValue_actionPerformed() { try { @@ -257,27 +290,34 @@ public abstract class AnnotationRowFilter extends JPanel } } - public void thresholdIsMin_actionPerformed() + protected void thresholdIsMin_actionPerformed() { updateView(); } - protected void populateThresholdComboBox(JComboBox threshold) + protected void populateThresholdComboBox(JComboBox thresh) { - threshold.addItem(MessageManager + thresh.addItem(MessageManager .getString("label.threshold_feature_no_threshold")); - threshold.addItem(MessageManager + thresh.addItem(MessageManager .getString("label.threshold_feature_above_threshold")); - threshold.addItem(MessageManager + thresh.addItem(MessageManager .getString("label.threshold_feature_below_threshold")); } - protected void seqAssociated_actionPerformed(JComboBox annotations) + /** + * Rebuilds the drop-down list of annotations to choose from when the 'per + * sequence only' checkbox is checked or unchecked. + * + * @param anns + */ + protected void seqAssociated_actionPerformed(JComboBox anns) { adjusting = true; - String cursel = (String) annotations.getSelectedItem(); - boolean isvalid = false, isseqs = seqAssociated.isSelected(); - annotations.removeAllItems(); + String cursel = (String) anns.getSelectedItem(); + boolean isvalid = false; + boolean isseqs = seqAssociated.isSelected(); + anns.removeAllItems(); for (String anitem : getAnnotationItems(seqAssociated.isSelected())) { if (anitem.equals(cursel) || (isseqs && cursel.startsWith(anitem))) @@ -285,20 +325,22 @@ public abstract class AnnotationRowFilter extends JPanel isvalid = true; cursel = anitem; } - annotations.addItem(anitem); + anns.addItem(anitem); } - adjusting = false; if (isvalid) { - annotations.setSelectedItem(cursel); + anns.setSelectedItem(cursel); } else { - if (annotations.getItemCount() > 0) + if (anns.getItemCount() > 0) { - annotations.setSelectedIndex(0); + anns.setSelectedIndex(0); } } + adjusting = false; + + updateView(); } protected void propagateSeqAssociatedThreshold(boolean allAnnotation, @@ -329,76 +371,107 @@ public abstract class AnnotationRowFilter extends JPanel } } - protected boolean colorAlignmContaining(AlignmentAnnotation currentAnn, - int selectedThresholdOption) + public AlignmentAnnotation getCurrentAnnotation() { + return currentAnnotation; + } - AnnotationColourGradient acg = null; - if (currentColours.isSelected()) - { - acg = new AnnotationColourGradient(currentAnn, - av.getGlobalColourScheme(), selectedThresholdOption); - } - else - { - acg = new AnnotationColourGradient(currentAnn, - minColour.getBackground(), maxColour.getBackground(), - selectedThresholdOption); - } - acg.setSeqAssociated(seqAssociated.isSelected()); + protected void setCurrentAnnotation(AlignmentAnnotation currentAnnotation) + { + this.currentAnnotation = currentAnnotation; + } - if (currentAnn.graphMin == 0f && currentAnn.graphMax == 0f) - { - acg.setPredefinedColours(true); - } + protected abstract void valueChanged(boolean updateAllAnnotation); - acg.thresholdIsMinMax = thresholdIsMin.isSelected(); + protected abstract void updateView(); - av.setGlobalColourScheme(acg); + protected abstract void reset(); - if (av.getAlignment().getGroups() != null) + protected String getAnnotationMenuLabel(AlignmentAnnotation ann) + { + return annotationLabels.get(ann); + } + + protected void jbInit() + { + ok.setOpaque(false); + ok.setText(MessageManager.getString("action.ok")); + ok.addActionListener(new ActionListener() { + @Override + public void actionPerformed(ActionEvent e) + { + ok_actionPerformed(); + } + }); - for (SequenceGroup sg : ap.av.getAlignment().getGroups()) + cancel.setOpaque(false); + cancel.setText(MessageManager.getString("action.cancel")); + cancel.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) { - if (sg.cs == null) - { - continue; - } + cancel_actionPerformed(); + } + }); - AnnotationColourGradient scheme = null; - if (currentColours.isSelected()) - { - scheme = new AnnotationColourGradient(currentAnn, - sg.getColourScheme(), selectedThresholdOption); - } - else - { - scheme = new AnnotationColourGradient(currentAnn, - minColour.getBackground(), maxColour.getBackground(), - selectedThresholdOption); - } - scheme.setSeqAssociated(seqAssociated.isSelected()); - sg.setColourScheme(scheme); + annotations.addItemListener(new ItemListener() + { + @Override + public void itemStateChanged(ItemEvent e) + { + selectedAnnotationChanged(); } - } - return false; + }); + annotations.setToolTipText(MessageManager + .getString("info.select_annotation_row")); + + threshold.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + threshold_actionPerformed(); + } + }); + + thresholdValue.setEnabled(false); + thresholdValue.setColumns(7); + thresholdValue.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + thresholdValue_actionPerformed(); + } + }); + + slider.setPaintLabels(false); + slider.setPaintTicks(true); + slider.setBackground(Color.white); + slider.setEnabled(false); + slider.setOpaque(false); + slider.setPreferredSize(new Dimension(100, 32)); } - public jalview.datamodel.AlignmentAnnotation getCurrentAnnotation() + public JComboBox getThreshold() { - return currentAnnotation; + return threshold; } - public void setCurrentAnnotation( - jalview.datamodel.AlignmentAnnotation currentAnnotation) + public void setThreshold(JComboBox thresh) { - this.currentAnnotation = currentAnnotation; + this.threshold = thresh; } - public abstract void valueChanged(boolean updateAllAnnotation); - - public abstract void updateView(); + public JComboBox getAnnotations() + { + return annotations; + } - public abstract void reset(); + public void setAnnotations(JComboBox anns) + { + this.annotations = anns; + } } diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index 3ac453f..5217ae7 100644 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -29,6 +29,7 @@ import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; +import jalview.datamodel.GraphLine; import jalview.datamodel.PDBEntry; import jalview.datamodel.RnaViewerModel; import jalview.datamodel.SequenceGroup; @@ -77,7 +78,6 @@ import jalview.schemes.AnnotationColourGradient; import jalview.schemes.ColourSchemeI; import jalview.schemes.ColourSchemeProperty; import jalview.schemes.FeatureColour; -import jalview.schemes.ResidueColourScheme; import jalview.schemes.ResidueProperties; import jalview.schemes.UserColourScheme; import jalview.structure.StructureSelectionManager; @@ -1711,6 +1711,15 @@ public class Jalview2XML return matchedFile; } + /** + * Populates the AnnotationColours xml for save. This captures the settings of + * the options in the 'Colour by Annotation' dialog. + * + * @param acg + * @param userColours + * @param jms + * @return + */ private AnnotationColours constructAnnotationColours( AnnotationColourGradient acg, List userColours, JalviewModelSequence jms) @@ -1718,8 +1727,9 @@ public class Jalview2XML AnnotationColours ac = new AnnotationColours(); ac.setAboveThreshold(acg.getAboveThreshold()); ac.setThreshold(acg.getAnnotationThreshold()); - ac.setAnnotation(acg.getAnnotation()); - if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme) + // 2.10.2 save annotationId (unique) not annotation label + ac.setAnnotation(acg.getAnnotation().annotationId); + if (acg.getBaseColour() instanceof UserColourScheme) { ac.setColourScheme(setUserColourScheme(acg.getBaseColour(), userColours, jms)); @@ -2639,10 +2649,12 @@ public class Jalview2XML @Override public void run() { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, - finalErrorMessage, "Error " - + (saving ? "saving" : "loading") - + " Jalview file", JvOptionPane.WARNING_MESSAGE); + JvOptionPane + .showInternalMessageDialog(Desktop.desktop, + finalErrorMessage, "Error " + + (saving ? "saving" : "loading") + + " Jalview file", + JvOptionPane.WARNING_MESSAGE); } }); } @@ -4689,12 +4701,21 @@ public class Jalview2XML return af; } + /** + * Reads saved data to restore Colour by Annotation settings + * + * @param viewAnnColour + * @param af + * @param al + * @param jms + * @param checkGroupAnnColour + * @return + */ private ColourSchemeI constructAnnotationColour( AnnotationColours viewAnnColour, AlignFrame af, AlignmentI al, JalviewModelSequence jms, boolean checkGroupAnnColour) { boolean propagateAnnColour = false; - ColourSchemeI cs = null; AlignmentI annAlignment = af != null ? af.viewport.getAlignment() : al; if (checkGroupAnnColour && al.getGroups() != null && al.getGroups().size() > 0) @@ -4702,7 +4723,7 @@ public class Jalview2XML // pre 2.8.1 behaviour // check to see if we should transfer annotation colours propagateAnnColour = true; - for (jalview.datamodel.SequenceGroup sg : al.getGroups()) + for (SequenceGroup sg : al.getGroups()) { if (sg.getColourScheme() instanceof AnnotationColourGradient) { @@ -4710,107 +4731,84 @@ public class Jalview2XML } } } - // int find annotation - if (annAlignment.getAlignmentAnnotation() != null) + + /* + * 2.10.2- : saved annotationId is AlignmentAnnotation.annotationId + */ + String annotationId = viewAnnColour.getAnnotation(); + AlignmentAnnotation matchedAnnotation = annotationIds.get(annotationId); + + /* + * pre 2.10.2: saved annotationId is AlignmentAnnotation.label + */ + if (matchedAnnotation == null && annAlignment.getAlignmentAnnotation() != null) { for (int i = 0; i < annAlignment.getAlignmentAnnotation().length; i++) { - if (annAlignment.getAlignmentAnnotation()[i].label - .equals(viewAnnColour.getAnnotation())) + if (annotationId + .equals(annAlignment.getAlignmentAnnotation()[i].label)) { - if (annAlignment.getAlignmentAnnotation()[i].getThreshold() == null) - { - annAlignment.getAlignmentAnnotation()[i] - .setThreshold(new jalview.datamodel.GraphLine( - viewAnnColour.getThreshold(), "Threshold", - java.awt.Color.black) - - ); - } - - if (viewAnnColour.getColourScheme().equals( - ResidueColourScheme.NONE)) - { - cs = new AnnotationColourGradient( - annAlignment.getAlignmentAnnotation()[i], - new java.awt.Color(viewAnnColour.getMinColour()), - new java.awt.Color(viewAnnColour.getMaxColour()), - viewAnnColour.getAboveThreshold()); - } - else if (viewAnnColour.getColourScheme().startsWith("ucs")) - { - cs = new AnnotationColourGradient( - annAlignment.getAlignmentAnnotation()[i], - getUserColourScheme(jms, - viewAnnColour.getColourScheme()), - viewAnnColour.getAboveThreshold()); - } - else - { - cs = new AnnotationColourGradient( - annAlignment.getAlignmentAnnotation()[i], - ColourSchemeProperty.getColourScheme(al, - viewAnnColour.getColourScheme()), - viewAnnColour.getAboveThreshold()); - } - if (viewAnnColour.hasPerSequence()) - { - ((AnnotationColourGradient) cs).setSeqAssociated(viewAnnColour - .isPerSequence()); - } - if (viewAnnColour.hasPredefinedColours()) - { - ((AnnotationColourGradient) cs) - .setPredefinedColours(viewAnnColour - .isPredefinedColours()); - } - if (propagateAnnColour && al.getGroups() != null) - { - // Also use these settings for all the groups - for (int g = 0; g < al.getGroups().size(); g++) - { - jalview.datamodel.SequenceGroup sg = al.getGroups().get(g); - - if (sg.cs == null) - { - continue; - } + matchedAnnotation = annAlignment.getAlignmentAnnotation()[i]; + break; + } + } + } + if (matchedAnnotation == null) + { + System.err.println("Failed to match annotation colour scheme for " + + annotationId); + return null; + } + if (matchedAnnotation.getThreshold() == null) + { + matchedAnnotation.setThreshold(new GraphLine(viewAnnColour.getThreshold(), + "Threshold", Color.black)); + } - /* - * if (viewAnnColour.getColourScheme().equals(ResidueColourScheme.NONE)) { sg.cs = - * new AnnotationColourGradient( - * annAlignment.getAlignmentAnnotation()[i], new - * java.awt.Color(viewAnnColour. getMinColour()), new - * java.awt.Color(viewAnnColour. getMaxColour()), - * viewAnnColour.getAboveThreshold()); } else - */ - { - sg.setColourScheme(new AnnotationColourGradient( - annAlignment.getAlignmentAnnotation()[i], sg - .getColourScheme(), viewAnnColour - .getAboveThreshold())); - if (cs instanceof AnnotationColourGradient) - { - if (viewAnnColour.hasPerSequence()) - { - ((AnnotationColourGradient) cs) - .setSeqAssociated(viewAnnColour.isPerSequence()); - } - if (viewAnnColour.hasPredefinedColours()) - { - ((AnnotationColourGradient) cs) - .setPredefinedColours(viewAnnColour - .isPredefinedColours()); - } - } - } + AnnotationColourGradient cs = null; + if (viewAnnColour.getColourScheme().equals("None")) + { + cs = new AnnotationColourGradient(matchedAnnotation, new Color( + viewAnnColour.getMinColour()), new Color( + viewAnnColour.getMaxColour()), + viewAnnColour.getAboveThreshold()); + } + else if (viewAnnColour.getColourScheme().startsWith("ucs")) + { + cs = new AnnotationColourGradient(matchedAnnotation, getUserColourScheme( + jms, viewAnnColour.getColourScheme()), + viewAnnColour.getAboveThreshold()); + } + else + { + cs = new AnnotationColourGradient(matchedAnnotation, + ColourSchemeProperty.getColourScheme(al, + viewAnnColour.getColourScheme()), + viewAnnColour.getAboveThreshold()); + } - } - } + boolean perSequenceOnly = viewAnnColour.isPerSequence(); + boolean useOriginalColours = viewAnnColour.isPredefinedColours(); + cs.setSeqAssociated(perSequenceOnly); + cs.setPredefinedColours(useOriginalColours); - break; + if (propagateAnnColour && al.getGroups() != null) + { + // Also use these settings for all the groups + for (int g = 0; g < al.getGroups().size(); g++) + { + SequenceGroup sg = al.getGroups().get(g); + if (sg.getGroupColourScheme() == null) + { + continue; } + AnnotationColourGradient groupScheme = new AnnotationColourGradient( + matchedAnnotation, sg.getColourScheme(), + viewAnnColour.getAboveThreshold()); + sg.setColourScheme(groupScheme); + groupScheme.setSeqAssociated(perSequenceOnly); + groupScheme.setPredefinedColours(useOriginalColours); } } return cs; diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 81c3d4f..d91fa70 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -43,7 +43,6 @@ import jalview.io.FileFormatI; import jalview.io.FileFormats; import jalview.io.FormatAdapter; import jalview.io.SequenceAnnotationReport; -import jalview.schemes.AnnotationColourGradient; import jalview.schemes.Blosum62ColourScheme; import jalview.schemes.ColourSchemeI; import jalview.schemes.ColourSchemes; @@ -1179,12 +1178,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener hideInsertions_actionPerformed(e); } }); - /* - * annotationMenuItem.setText("By Annotation"); - * annotationMenuItem.addActionListener(new ActionListener() { public void - * actionPerformed(ActionEvent actionEvent) { - * annotationMenuItem_actionPerformed(actionEvent); } }); - */ + groupMenu.add(sequenceSelDetails); add(groupMenu); add(sequenceMenu); @@ -1620,24 +1614,6 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener refresh(); } - public void annotationMenuItem_actionPerformed(ActionEvent actionEvent) - { - SequenceGroup sg = getGroup(); - if (sg == null) - { - return; - } - - AnnotationColourGradient acg = new AnnotationColourGradient( - sequence.getAnnotation()[0], null, - AnnotationColourGradient.NO_THRESHOLD); - - acg.setPredefinedColours(true); - sg.setColourScheme(acg); - - refresh(); - } - /** * DOCUMENT ME! * diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java index 1a3e9ef..a5d779d 100755 --- a/src/jalview/schemes/AnnotationColourGradient.java +++ b/src/jalview/schemes/AnnotationColourGradient.java @@ -27,6 +27,8 @@ import jalview.datamodel.Annotation; import jalview.datamodel.GraphLine; import jalview.datamodel.SequenceCollectionI; import jalview.datamodel.SequenceI; +import jalview.renderer.AnnotationRenderer; +import jalview.util.Comparison; import java.awt.Color; import java.util.IdentityHashMap; @@ -40,15 +42,25 @@ public class AnnotationColourGradient extends FollowerColourScheme public static final int ABOVE_THRESHOLD = 1; - public AlignmentAnnotation annotation; + private final AlignmentAnnotation annotation; - int aboveAnnotationThreshold = -1; + private final int aboveAnnotationThreshold; public boolean thresholdIsMinMax = false; - GraphLine annotationThreshold; + private GraphLine annotationThreshold; - float r1, g1, b1, rr, gg, bb; + private int redMin; + + private int greenMin; + + private int blueMin; + + private int redRange; + + private int greenRange; + + private int blueRange; private boolean predefinedColours = false; @@ -61,7 +73,7 @@ public class AnnotationColourGradient extends FollowerColourScheme */ private boolean noGradient = false; - IdentityHashMap seqannot = null; + private IdentityHashMap seqannot = null; @Override public ColourSchemeI getInstance(AnnotatedCollectionI sg, @@ -72,12 +84,12 @@ public class AnnotationColourGradient extends FollowerColourScheme acg.thresholdIsMinMax = thresholdIsMinMax; acg.annotationThreshold = (annotationThreshold == null) ? null : new GraphLine(annotationThreshold); - acg.r1 = r1; - acg.g1 = g1; - acg.b1 = b1; - acg.rr = rr; - acg.gg = gg; - acg.bb = bb; + acg.redMin = redMin; + acg.greenMin = greenMin; + acg.blueMin = blueMin; + acg.redRange = redRange; + acg.greenRange = greenRange; + acg.blueRange = blueRange; acg.predefinedColours = predefinedColours; acg.seqAssociated = seqAssociated; acg.noGradient = noGradient; @@ -109,12 +121,12 @@ public class AnnotationColourGradient extends FollowerColourScheme annotationThreshold = annotation.threshold; } // clear values so we don't get weird black bands... - r1 = 254; - g1 = 254; - b1 = 254; - rr = 0; - gg = 0; - bb = 0; + redMin = 254; + greenMin = 254; + blueMin = 254; + redRange = 0; + greenRange = 0; + blueRange = 0; noGradient = true; checkLimits(); @@ -135,13 +147,13 @@ public class AnnotationColourGradient extends FollowerColourScheme annotationThreshold = annotation.threshold; } - r1 = minColour.getRed(); - g1 = minColour.getGreen(); - b1 = minColour.getBlue(); + redMin = minColour.getRed(); + greenMin = minColour.getGreen(); + blueMin = minColour.getBlue(); - rr = maxColour.getRed() - r1; - gg = maxColour.getGreen() - g1; - bb = maxColour.getBlue() - b1; + redRange = maxColour.getRed() - redMin; + greenRange = maxColour.getGreen() - greenMin; + blueRange = maxColour.getBlue() - blueMin; noGradient = false; checkLimits(); @@ -211,9 +223,9 @@ public class AnnotationColourGradient extends FollowerColourScheme float aamin = 0f, aamax = 0f; - public String getAnnotation() + public AlignmentAnnotation getAnnotation() { - return annotation.label; + return annotation; } public int getAboveThreshold() @@ -235,12 +247,13 @@ public class AnnotationColourGradient extends FollowerColourScheme public Color getMinColour() { - return new Color((int) r1, (int) g1, (int) b1); + return new Color(redMin, greenMin, blueMin); } public Color getMaxColour() { - return new Color((int) (r1 + rr), (int) (g1 + gg), (int) (b1 + bb)); + return new Color(redMin + redRange, greenMin + greenRange, blueMin + + blueRange); } /** @@ -258,137 +271,157 @@ public class AnnotationColourGradient extends FollowerColourScheme } /** - * DOCUMENT ME! + * Returns the colour for a given character and position in a sequence * - * @param n - * DOCUMENT ME! + * @param c + * the residue character * @param j - * DOCUMENT ME! - * - * @return DOCUMENT ME! + * the aligned position + * @param seq + * the sequence + * @return */ @Override public Color findColour(char c, int j, SequenceI seq) { - Color currentColour = Color.white; - AlignmentAnnotation annotation = (seqAssociated && seqannot != null ? seqannot + /* + * locate the annotation we are configured to colour by + */ + AlignmentAnnotation ann = (seqAssociated && seqannot != null ? seqannot .get(seq) : this.annotation); - if (annotation == null) + + /* + * if gap or no annotation at position, no colour (White) + */ + if (ann == null || ann.annotations == null + || j >= ann.annotations.length || ann.annotations[j] == null + || Comparison.isGap(c)) { - return currentColour; + return Color.white; } - // if ((threshold == 0) || aboveThreshold(c, j)) - // { - if (annotation.annotations != null && j < annotation.annotations.length - && annotation.annotations[j] != null - && !jalview.util.Comparison.isGap(c)) + + Annotation aj = ann.annotations[j]; + // 'use original colours' => colourScheme != null + // -> look up colour to be used + // predefined colours => preconfigured shading + // -> only use original colours reference if thresholding enabled & + // minmax exists + // annotation.hasIcons => null or black colours replaced with glyph + // colours + // -> reuse original colours if present + // -> if thresholding enabled then return colour on non-whitespace glyph + + /* + * if threshold applies, and annotation fails the test - no colour (white) + */ + if (annotationThreshold != null) { - Annotation aj = annotation.annotations[j]; - // 'use original colours' => colourScheme != null - // -> look up colour to be used - // predefined colours => preconfigured shading - // -> only use original colours reference if thresholding enabled & - // minmax exists - // annotation.hasIcons => null or black colours replaced with glyph - // colours - // -> reuse original colours if present - // -> if thresholding enabled then return colour on non-whitespace glyph - - if (aboveAnnotationThreshold == NO_THRESHOLD - || (annotationThreshold != null && (aboveAnnotationThreshold == ABOVE_THRESHOLD ? aj.value >= annotationThreshold.value - : aj.value <= annotationThreshold.value))) + if ((aboveAnnotationThreshold == ABOVE_THRESHOLD && aj.value >= annotationThreshold.value) + || (aboveAnnotationThreshold == BELOW_THRESHOLD && aj.value > annotationThreshold.value)) { - if (predefinedColours && aj.colour != null - && !aj.colour.equals(Color.black)) - { - currentColour = aj.colour; - } - else if (annotation.hasIcons - && annotation.graph == AlignmentAnnotation.NO_GRAPH) + return Color.white; + } + } + + /* + * If 'use original colours' then return the colour of the annotation + * at the aligned position - computed using the background colour scheme + */ + if (predefinedColours && aj.colour != null + && !aj.colour.equals(Color.black)) + { + return aj.colour; + } + + Color result = Color.white; + if (ann.hasIcons && ann.graph == AlignmentAnnotation.NO_GRAPH) + { + /* + * secondary structure symbol colouring + */ + if (aj.secondaryStructure > ' ' && aj.secondaryStructure != '.' + && aj.secondaryStructure != '-') + { + if (getColourScheme() != null) { - if (aj.secondaryStructure > ' ' && aj.secondaryStructure != '.' - && aj.secondaryStructure != '-') - { - if (getColourScheme() != null) - { - currentColour = getColourScheme().findColour(c, j, seq, null, - 0f); - } - else - { - if (annotation.isRNA()) - { - currentColour = ColourSchemeProperty.rnaHelices[(int) aj.value]; - } - else - { - currentColour = annotation.annotations[j].secondaryStructure == 'H' ? jalview.renderer.AnnotationRenderer.HELIX_COLOUR - : annotation.annotations[j].secondaryStructure == 'E' ? jalview.renderer.AnnotationRenderer.SHEET_COLOUR - : jalview.renderer.AnnotationRenderer.STEM_COLOUR; - } - } - } - else - { - // - return Color.white; - } + result = getColourScheme().findColour(c, j, seq, null, 0f); } - else if (noGradient) + else { - if (getColourScheme() != null) + if (ann.isRNA()) { - currentColour = getColourScheme().findColour(c, j, seq, null, - 0f); + result = ColourSchemeProperty.rnaHelices[(int) aj.value]; } else { - if (aj.colour != null) - { - currentColour = aj.colour; - } + result = ann.annotations[j].secondaryStructure == 'H' ? AnnotationRenderer.HELIX_COLOUR + : ann.annotations[j].secondaryStructure == 'E' ? AnnotationRenderer.SHEET_COLOUR + : AnnotationRenderer.STEM_COLOUR; } } - else + } + else + { + return Color.white; + } + } + else if (noGradient) + { + if (getColourScheme() != null) + { + result = getColourScheme().findColour(c, j, seq, null, 0f); + } + else + { + if (aj.colour != null) { - currentColour = shadeCalculation(annotation, j); + result = aj.colour; } } - // if (conservationColouring) - // { - // currentColour = applyConservation(currentColour, j); - // } } - // } - return currentColour; + else + { + result = shadeCalculation(ann, j); + } + + return result; } - private Color shadeCalculation(AlignmentAnnotation annotation, int j) + /** + * Returns a graduated colour for the annotation at the given column. If there + * is a threshold value, and it is used as the top/bottom of the colour range, + * and the value satisfies the threshold condition, then a colour + * proportionate to the range from the threshold is calculated. For all other + * cases, a colour proportionate to the annotation's min-max range is + * calulated. Note that thresholding is _not_ done here (a colour is computed + * even if threshold is not passed). + * + * @param ann + * @param col + * @return + */ + Color shadeCalculation(AlignmentAnnotation ann, int col) { - - // calculate a shade float range = 1f; - if (thresholdIsMinMax - && annotation.threshold != null + float value = ann.annotations[col].value; + if (thresholdIsMinMax && ann.threshold != null && aboveAnnotationThreshold == ABOVE_THRESHOLD - && annotation.annotations[j].value >= annotation.threshold.value) + && value >= ann.threshold.value) { - range = (annotation.annotations[j].value - annotation.threshold.value) - / (annotation.graphMax - annotation.threshold.value); + range = (value - ann.threshold.value) + / (ann.graphMax - ann.threshold.value); } - else if (thresholdIsMinMax && annotation.threshold != null + else if (thresholdIsMinMax && ann.threshold != null && aboveAnnotationThreshold == BELOW_THRESHOLD - && annotation.annotations[j].value >= annotation.graphMin) + && value <= ann.threshold.value) { - range = (annotation.annotations[j].value - annotation.graphMin) - / (annotation.threshold.value - annotation.graphMin); + range = (value - ann.graphMin) / (ann.threshold.value - ann.graphMin); } else { - if (annotation.graphMax != annotation.graphMin) + if (ann.graphMax != ann.graphMin) { - range = (annotation.annotations[j].value - annotation.graphMin) - / (annotation.graphMax - annotation.graphMin); + range = (value - ann.graphMin) / (ann.graphMax - ann.graphMin); } else { @@ -396,11 +429,11 @@ public class AnnotationColourGradient extends FollowerColourScheme } } - int dr = (int) (rr * range + r1), dg = (int) (gg * range + g1), db = (int) (bb - * range + b1); + int dr = (int) (redRange * range + redMin); + int dg = (int) (greenRange * range + greenMin); + int db = (int) (blueRange * range + blueMin); return new Color(dr, dg, db); - } public boolean isPredefinedColours() @@ -423,6 +456,16 @@ public class AnnotationColourGradient extends FollowerColourScheme seqAssociated = sassoc; } + public boolean isThresholdIsMinMax() + { + return thresholdIsMinMax; + } + + public void setThresholdIsMinMax(boolean minMax) + { + this.thresholdIsMinMax = minMax; + } + @Override public String getSchemeName() { diff --git a/test/jalview/gui/AnnotationRowFilterTest.java b/test/jalview/gui/AnnotationRowFilterTest.java new file mode 100644 index 0000000..2785639 --- /dev/null +++ b/test/jalview/gui/AnnotationRowFilterTest.java @@ -0,0 +1,119 @@ +package jalview.gui; + +import static org.testng.Assert.assertEquals; + +import java.util.Vector; + +import jalview.bin.Cache; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.SequenceI; +import jalview.io.DataSourceType; +import jalview.io.FileLoader; + +import org.testng.annotations.BeforeClass; +import org.testng.annotations.Test; + +/** + * Tests for methods of base class of annotation column or colour chooser + */ +public class AnnotationRowFilterTest +{ + AlignFrame af; + + private AnnotationRowFilter testee; + + @BeforeClass(alwaysRun = true) + public void setUp() + { + Cache.loadProperties("test/jalview/io/testProps.jvprops"); + Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", + Boolean.TRUE.toString()); + af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa", + DataSourceType.FILE); + testee = new AnnotationRowFilter(af.viewport, af.alignPanel) + { + @Override + public void valueChanged(boolean updateAllAnnotation) + { + } + + @Override + public void updateView() + { + } + + @Override + public void reset() + { + } + }; + } + + /** + * Test the method that builds the drop-down list of annotations to choose + * from for colour by annotation or select columns by annotation + */ + @Test(groups = "Functional") + public void testGetAnnotationItems() + { + AlignmentI al = af.getViewport().getAlignment(); + SequenceI seq1 = al.findSequenceMatch("FER_CAPAA")[0]; + SequenceI seq2 = al.findSequenceMatch("FER_BRANA")[0]; + + AlignmentAnnotation ann1 = new AlignmentAnnotation("ann1Label", "ann1", + null); + al.addAnnotation(ann1); + AlignmentAnnotation ann2 = new AlignmentAnnotation("Significance", + "ann2", null); + al.addAnnotation(ann2); + /* + * a second Significance alignment annotation + */ + AlignmentAnnotation ann2a = new AlignmentAnnotation("Significance", + "ann2", null); + al.addAnnotation(ann2a); + + AlignmentAnnotation ann3 = new AlignmentAnnotation("Jronn", "Jronn", + null); + ann3.setSequenceRef(seq1); + al.addAnnotation(ann3); + AlignmentAnnotation ann4 = new AlignmentAnnotation("Jronn", "Jronn", + null); + ann4.setSequenceRef(seq2); + al.addAnnotation(ann4); + AlignmentAnnotation ann5 = new AlignmentAnnotation("Jnet", "Jnet", null); + ann5.setSequenceRef(seq2); + al.addAnnotation(ann5); + /* + * a second Jnet annotation for FER_BRANA + */ + AlignmentAnnotation ann6 = new AlignmentAnnotation("Jnet", "Jnet", null); + ann6.setSequenceRef(seq2); + al.addAnnotation(ann6); + + /* + * drop-down items with 'Per-sequence only' not checked + */ + Vector items = testee.getAnnotationItems(false); + assertEquals( + items.toString(), + "[Conservation, Quality, Consensus, ann1Label, Significance, Significance_1, Jronn_FER_CAPAA, Jronn_FER_BRANA, Jnet_FER_BRANA, Jnet_FER_BRANA_2]"); + assertEquals(testee.getAnnotationMenuLabel(ann1), "ann1Label"); + assertEquals(testee.getAnnotationMenuLabel(ann2), "Significance"); + assertEquals(testee.getAnnotationMenuLabel(ann2a), "Significance_1"); + assertEquals(testee.getAnnotationMenuLabel(ann3), "Jronn_FER_CAPAA"); + assertEquals(testee.getAnnotationMenuLabel(ann4), "Jronn_FER_BRANA"); + assertEquals(testee.getAnnotationMenuLabel(ann5), "Jnet_FER_BRANA"); + assertEquals(testee.getAnnotationMenuLabel(ann6), "Jnet_FER_BRANA_2"); + + /* + * drop-down items with 'Per-sequence only' checked + */ + items = testee.getAnnotationItems(true); + assertEquals(items.toString(), "[Jronn, Jnet]"); + // the first annotation of the type is associated with the menu item + assertEquals(testee.getAnnotationMenuLabel(ann3), "Jronn"); + assertEquals(testee.getAnnotationMenuLabel(ann5), "Jnet"); + } +} diff --git a/test/jalview/schemes/AnnotationColourGradientTest.java b/test/jalview/schemes/AnnotationColourGradientTest.java new file mode 100644 index 0000000..42e3eb4 --- /dev/null +++ b/test/jalview/schemes/AnnotationColourGradientTest.java @@ -0,0 +1,168 @@ +package jalview.schemes; + +import static org.testng.Assert.assertEquals; + +import java.awt.Color; + +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.Annotation; +import jalview.datamodel.GraphLine; + +import org.testng.annotations.BeforeClass; +import org.testng.annotations.Test; + +public class AnnotationColourGradientTest +{ + final static int WIDTH = 11; + + final static int THRESHOLD = 5; + + private AlignmentAnnotation ann; + + Color minColour = new Color(50, 200, 150); + + Color maxColour = new Color(150, 100, 250); + + @BeforeClass + public void setUp() + { + Annotation[] anns = new Annotation[WIDTH]; + /* + * set annotations with values 0-10 + */ + for (int col = 0; col < WIDTH; col++) + { + anns[col] = new Annotation("a", "a", 'a', col); + } + + /* + * AlignmentAnnotation constructor works out min-max range + */ + ann = new AlignmentAnnotation("", "", anns); + ann.setThreshold(new GraphLine(THRESHOLD, "", Color.RED)); + } + + @Test(groups = "Functional") + public void testShadeCalculation_noThreshold() + { + AnnotationColourGradient testee = new AnnotationColourGradient(ann, + minColour, maxColour, AnnotationColourGradient.NO_THRESHOLD); + for (int col = 0; col < WIDTH; col++) + { + Color result = testee.shadeCalculation(ann, col); + /* + * column is n/10 of the way from minCol to maxCol + */ + Color expected = new Color(50 + 10 * col, 200 - 10 * col, + 150 + 10 * col); + assertEquals(result, expected, "for column " + col); + } + } + + /** + * Test the 'colour above threshold' case + */ + @Test(groups = "Functional") + public void testShadeCalculation_aboveThreshold() + { + AnnotationColourGradient testee = new AnnotationColourGradient(ann, + minColour, maxColour, AnnotationColourGradient.ABOVE_THRESHOLD); + for (int col = 0; col < WIDTH; col++) + { + Color result = testee.shadeCalculation(ann, col); + /* + * colour is derived regardless of the threshold value + * (the renderer that will suppress colouring if + * above/below threshold) + */ + Color expected = new Color(50 + 10 * col, 200 - 10 * col, + 150 + 10 * col); + assertEquals(result, expected, "for column " + col); + } + + /* + * now make 6-10 the span of the colour range + * (annotation value == column number in this test) + */ + testee.setThresholdIsMinMax(true); + for (int col = 0; col < THRESHOLD; col++) + { + /* + * colours below the threshold are computed as before + */ + Color expected = new Color(50 + 10 * col, 200 - 10 * col, + 150 + 10 * col); + Color result = testee.shadeCalculation(ann, col); + assertEquals(result, expected, "for column " + col); + } + for (int col = THRESHOLD; col < WIDTH; col++) + { + /* + * colours for values >= threshold are graduated + * range is 6-10 so steps of 100/5 = 20 + */ + int factor = col - THRESHOLD; + Color expected = new Color(50 + 20 * factor, 200 - 20 * factor, + 150 + 20 * factor); + Color result = testee.shadeCalculation(ann, col); + assertEquals(result, expected, "for column " + col); + } + } + + /** + * Test the 'colour below threshold' case + */ + @Test(groups = "Functional") + public void testShadeCalculation_belowThreshold() + { + /* + * change threshold to 5 so we have an easy calculation of + * the min-max range 0-5 + */ + int threshold = 5; + ann.setThreshold(new GraphLine(threshold, "", Color.RED)); + AnnotationColourGradient testee = new AnnotationColourGradient(ann, + minColour, maxColour, AnnotationColourGradient.BELOW_THRESHOLD); + + for (int col = 0; col < WIDTH; col++) + { + Color result = testee.shadeCalculation(ann, col); + /* + * colour is derived regardless of the threshold value + * (the renderer that will suppress colouring if + * above/below threshold) + */ + Color expected = new Color(50 + 10 * col, 200 - 10 * col, + 150 + 10 * col); + assertEquals(result, expected, "for column " + col); + } + + /* + * now make 0-5 the span of the colour range + * (annotation value == column number in this test) + */ + testee.setThresholdIsMinMax(true); + for (int col = threshold + 1; col < WIDTH; col++) + { + /* + * colours above the threshold are computed as before + */ + Color expected = new Color(50 + 10 * col, 200 - 10 * col, + 150 + 10 * col); + Color result = testee.shadeCalculation(ann, col); + assertEquals(result, expected, "for column " + col); + } + + for (int col = 0; col <= threshold; col++) + { + /* + * colours for values <= threshold are graduated + * range is 0-5 so steps of 100/5 = 20 + */ + Color expected = new Color(50 + 20 * col, 200 - 20 * col, + 150 + 20 * col); + Color result = testee.shadeCalculation(ann, col); + assertEquals(result, expected, "for column " + col); + } + } +}