X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationColourChooser.java;h=5a942f1e752b8b835723bdfec10b5626e5a8437c;hb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;hp=f53f55a453c9858325bad4e68ee72061e2647f87;hpb=1cc81e06ac2faa5ee4b8879e9fa019956e34259f;p=jalview.git diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java index f53f55a..5a942f1 100755 --- a/src/jalview/gui/AnnotationColourChooser.java +++ b/src/jalview/gui/AnnotationColourChooser.java @@ -54,7 +54,7 @@ public class AnnotationColourChooser extends JPanel 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) { @@ -95,20 +95,21 @@ public class AnnotationColourChooser extends JPanel // Always get default shading from preferences. setDefaultMinMax(); - + if (oldcs instanceof AnnotationColourGradient) { AnnotationColourGradient acg = (AnnotationColourGradient) oldcs; currentColours.setSelected(acg.predefinedColours); if (!acg.predefinedColours) { - minColour.setBackground(acg.getMinColour()); + minColour.setBackground(acg.getMinColour()); maxColour.setBackground(acg.getMaxColour()); } seqAssociated.setSelected(acg.isSeqAssociated()); } adjusting = true; - annotations = new JComboBox(getAnnotationItems(seqAssociated.isSelected())); + annotations = new JComboBox( + getAnnotationItems(seqAssociated.isSelected())); threshold.addItem("No Threshold"); threshold.addItem("Above Threshold"); @@ -118,21 +119,23 @@ public class AnnotationColourChooser extends JPanel { AnnotationColourGradient acg = (AnnotationColourGradient) oldcs; annotations.setSelectedItem(acg.getAnnotation()); - switch (acg.getAboveThreshold()) { + switch (acg.getAboveThreshold()) + { case AnnotationColourGradient.NO_THRESHOLD: - threshold.setSelectedItem("No Threshold"); + threshold.setSelectedItem("No Threshold"); break; case AnnotationColourGradient.ABOVE_THRESHOLD: - threshold.setSelectedItem("Above Threshold"); + threshold.setSelectedItem("Above Threshold"); break; case AnnotationColourGradient.BELOW_THRESHOLD: threshold.setSelectedItem("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.setSelected(acg.thresholdIsMinMax); - thresholdValue.setText(""+acg.getAnnotationThreshold()); + thresholdValue.setText("" + acg.getAnnotationThreshold()); } try @@ -150,29 +153,36 @@ public class AnnotationColourChooser extends JPanel } - private Vector getAnnotationItems(boolean isSeqAssociated) { + private Vector getAnnotationItems(boolean isSeqAssociated) + { Vector list = new Vector(); int index = 1; int[] anmap = new int[av.getAlignment().getAlignmentAnnotation().length]; - boolean enableSeqAss=false; + boolean enableSeqAss = false; for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++) { - if (av.getAlignment().getAlignmentAnnotation()[i].sequenceRef==null) + if (av.getAlignment().getAlignmentAnnotation()[i].sequenceRef == null) { if (isSeqAssociated) - { + { continue; - } - } else { - enableSeqAss=true; + } + } + else + { + enableSeqAss = true; } String label = av.getAlignment().getAlignmentAnnotation()[i].label; if (!list.contains(label)) - {anmap[list.size()] = i; + { + anmap[list.size()] = i; list.addElement(label); - - }else { - if (!isSeqAssociated) { + + } + else + { + if (!isSeqAssociated) + { anmap[list.size()] = i; list.addElement(label + "_" + (index++)); } @@ -180,13 +190,16 @@ public class AnnotationColourChooser extends JPanel } seqAssociated.setEnabled(enableSeqAss); annmap = new int[list.size()]; - System.arraycopy(anmap, 0, annmap, 0, annmap.length); + System.arraycopy(anmap, 0, annmap, 0, annmap.length); return list; } + private void setDefaultMinMax() { - minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange)); - maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red)); + minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", + Color.orange)); + maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", + Color.red)); } public AnnotationColourChooser() @@ -250,17 +263,18 @@ public class AnnotationColourChooser extends JPanel }); defColours.setOpaque(false); defColours.setText("Defaults"); - defColours.setToolTipText("Reset min and max colours to defaults from user preferences."); + defColours + .setToolTipText("Reset min and max colours to defaults from user preferences."); defColours.addActionListener(new ActionListener() { - + @Override public void actionPerformed(ActionEvent arg0) { resetColours_actionPerformed(arg0); } }); - + annotations.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -315,16 +329,16 @@ public class AnnotationColourChooser extends JPanel seqAssociated.setText("Per-sequence only"); seqAssociated.addActionListener(new ActionListener() { - + @Override public void actionPerformed(ActionEvent arg0) { seqAssociated_actionPerformed(arg0); } }); - + this.setLayout(borderLayout1); - jPanel2.setLayout(new MigLayout("","[left][center][right]","[][][]")); + jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]")); jPanel1.setBackground(Color.white); jPanel2.setBackground(Color.white); @@ -339,7 +353,7 @@ public class AnnotationColourChooser extends JPanel colpanel.add(maxColour); jPanel2.add(colpanel, "wrap"); jPanel2.add(threshold); - jPanel2.add(defColours,"skip 1, wrap"); + jPanel2.add(defColours, "skip 1, wrap"); jPanel2.add(thresholdIsMin); jPanel2.add(slider, "grow"); jPanel2.add(thresholdValue, "grow"); @@ -350,22 +364,28 @@ public class AnnotationColourChooser extends JPanel protected void seqAssociated_actionPerformed(ActionEvent arg0) { - adjusting=true; + adjusting = true; String cursel = (String) annotations.getSelectedItem(); - boolean isvalid=false,isseqs=seqAssociated.isSelected(); + boolean isvalid = false, isseqs = seqAssociated.isSelected(); this.annotations.removeAllItems(); - for (String anitem:getAnnotationItems(seqAssociated.isSelected())) + for (String anitem : getAnnotationItems(seqAssociated.isSelected())) { - if (anitem.equals( cursel) || (isseqs && cursel.startsWith(anitem))) + if (anitem.equals(cursel) || (isseqs && cursel.startsWith(anitem))) { - isvalid=true; - cursel=anitem; + isvalid = true; + cursel = anitem; } this.annotations.addItem(anitem); } - adjusting=false; - if (isvalid) { this.annotations.setSelectedItem(cursel); } else { - if (annotations.getItemCount()>0) { + adjusting = false; + if (isvalid) + { + this.annotations.setSelectedItem(cursel); + } + else + { + if (annotations.getItemCount() > 0) + { annotations.setSelectedIndex(0); } } @@ -378,23 +398,27 @@ public class AnnotationColourChooser extends JPanel } JComboBox annotations; + int[] annmap; + JPanel minColour = new JPanel(); JPanel maxColour = new JPanel(); + JButton defColours = new JButton(); + JButton ok = new JButton(); JButton cancel = new JButton(); JPanel jPanel1 = new JPanel(); + JPanel jPanel2 = new JPanel(); - + BorderLayout borderLayout1 = new BorderLayout(); JComboBox threshold = new JComboBox(); - JSlider slider = new JSlider(); JTextField thresholdValue = new JTextField(20); @@ -402,7 +426,7 @@ public class AnnotationColourChooser extends JPanel JCheckBox currentColours = new JCheckBox(); JCheckBox thresholdIsMin = new JCheckBox(); - + JCheckBox seqAssociated = new JCheckBox(); public void minColour_actionPerformed() @@ -512,8 +536,8 @@ public class AnnotationColourChooser extends JPanel if (av.getAlignment().getGroups() != null) { - - for (SequenceGroup sg:ap.av.getAlignment().getGroups()) + + for (SequenceGroup sg : ap.av.getAlignment().getGroups()) { if (sg.cs == null) { @@ -524,7 +548,8 @@ public class AnnotationColourChooser extends JPanel { sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs, aboveThreshold); - ((AnnotationColourGradient)sg.cs).setSeqAssociated(seqAssociated.isSelected()); + ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated + .isSelected()); } else @@ -532,13 +557,15 @@ public class AnnotationColourChooser extends JPanel sg.cs = new AnnotationColourGradient(currentAnnotation, minColour.getBackground(), maxColour.getBackground(), aboveThreshold); - ((AnnotationColourGradient)sg.cs).setSeqAssociated(seqAssociated.isSelected()); + ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated + .isSelected()); } } } ap.alignmentChanged(); - // ensure all associated views (overviews, structures, etc) are notified of updated colours. + // ensure all associated views (overviews, structures, etc) are notified of + // updated colours. ap.paintAlignment(true); } @@ -556,7 +583,7 @@ public class AnnotationColourChooser extends JPanel public void cancel_actionPerformed(ActionEvent e) { reset(); - // ensure all original colouring is propagated to listeners. + // ensure all original colouring is propagated to listeners. ap.paintAlignment(true); try { @@ -571,8 +598,8 @@ public class AnnotationColourChooser extends JPanel av.setGlobalColourScheme(oldcs); if (av.getAlignment().getGroups() != null) { - - for (SequenceGroup sg:ap.av.getAlignment().getGroups()) + + for (SequenceGroup sg : ap.av.getAlignment().getGroups()) { sg.cs = (ColourSchemeI) oldgroupColours.get(sg); }